| Software | Resource | Containers | Description | AI Tags | AI Research Discipline | AI Software Type | Documentation, Uses, and more |
|---|---|---|---|---|---|---|---|
| "gtdbtk=2.4.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| abricate | lcc | 1.0 | Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. | Antimicrobial Resistance, Genomic Analysis, Bacterial Genomics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| abyss | lcc | N/A | ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. Description Source: https://www.bcgsc.ca/resources/software/abyss |
Assembly, De Novo Assembly, Sequence Assembler, Large Genomes | Biological Sciences | Hpc Tool | Documentation, Uses, and more |
| adapterremoval | lcc | 1.0 | AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. | Bioinformatics, Hts Data Processing, Sequence Analysis | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| adios | lcc | N/A | The Adaptable IO System (ADIOS) | I/O, High Performance Computing, Data Management | High Performance Computing, Scientific Data Management | Library | Documentation, Uses, and more |
| admixture | lcc, mcc | 1.0 | ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. | genetics, population genetics, bioinformatics | Bioinformatics, Population Genetics | Statistical Software | Documentation, Uses, and more |
| advisor | ecc, lcc | N/A | Intel Advisor is a performance analysis tool designed to help developers optimize and parallelize their software on Intel architectures. It provides insights for efficient vectorization, threading, and offloading to accelerators, aiding in achieving maximum performance from applications. | Hpc, Performance Optimization, Parallel Computing | Engineering & Technology | Performance Optimization | Documentation, Uses, and more |
| afterqc | lcc | 1.0 | Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. | Quality Control, High-Throughput Sequencing Data, Next-Generation Sequencing | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| agat | lcc | 1.0 | Agat is a suite of tools to handle gene annotations in any GTF/GFF format | Genome Assembly, Annotation, Evaluation, Genomic Analysis | Genomics, Biological Sciences | Pipeline | Documentation, Uses, and more |
| agptools | mcc | 1.0 | The AGP format is a tab-separated table format describing how components of a genome assembly fit together. NCBI accepts assemblies for submission in the format of a fasta file giving the sequences of components (usually contigs) along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. | Genome Assembly | Bioinformatics | Documentation, Uses, and more | |
| allmaps | lcc | N/A | With Allmaps, you can georeference any map from any institution that supports IIIF. Allmaps doesn’t require complicated GIS infrastructure and it doesn’t need to generate XYZ map tiles. All that’s needed is a IIIF server. | Genomics, chromosome reconstruction, bioinformatics | Genome Assembly, Bioinformatics | assembly scaffolding tool | Documentation, Uses, and more |
| amber | lcc | N/A | Amber MD application | Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics | Documentation, Uses, and more |
| ambertools | lcc, mcc | 1.0 | Ambertools is a suite can of complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. | Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization | Biophysics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| anaconda | lcc | 1.0 | Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. | Data Science, Scientific Computing, Package Management, Python, R | Informatics, Analytics & Information Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| ancestry_hmm | lcc | 1.0 | ancestry_hmm is a hidden Markov model–based software tool for inferring local ancestry along the genome in admixed individuals using genotype or sequencing data. It identifies ancestry transitions and ancestry proportions by modeling recombination, allele frequencies, and admixture history. | Computational genomics, Population genetics | population-genetics | Documentation, Uses, and more | |
| angsd | lcc, mcc | 1.0 | Angsd is a software for analyzing next generation sequencing data. | Ngs Data Analysis, Genome-Wide Association Studies, Population Genomics, Genetic Variation | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| annoy | lcc | 1.0 | Annoy (Approximate Nearest Neighbors Oh Yeah) is a high-performance library for searching large, high-dimensional vector spaces using approximate nearest-neighbor queries. It is designed for extremely fast similarity search, making it ideal for recommendation engines, clustering, retrieval, and large-scale data mining or machine-learning applications. | Machine Learning, Data Science, Approximate Nearest Neighbors, High-Dimensional Data | Machine Learning, Data Mining | Library | Documentation, Uses, and more |
| ansysedt | lcc | N/A | Ansys Electronics Desktop Student offers free access to the industry gold-standard Ansys simulators for work with antenna, RF, microwave, PCB, IC and IC package designs, along with electromechanical devices such as electric motors and generators. Students will have access to Ansys HFSS, Ansys Maxwell, Ansys Q3D, Ansys Icepak, Ansys Twin Builder, and Ansys Circuit, allowing design work on a broad range of electrical and electromechanical systems. | Electrical Engineering, Computational Electromagnetics | Electromagnetic Simulation Software | Documentation, Uses, and more | |
| antismash | mcc | 1.0 | Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. | Bioinformatics, Genome Mining, Biosynthetic Gene Clusters, Secondary Metabolites | Bioinformatics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| anvio | lcc, mcc | 1.0 | Anvio is an analysis and visualization platform for 'omics data. | Omics Data Analysis, Microbiome, Metagenomics, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ape | lcc | 1.0 | Documentation, Uses, and more | ||||
| apptainer | ecc | N/A | Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments. Description Source: https://apptainer.org/ |
Containerization, Application Management, Devops, Software Development | Engineering & Technology | Development | Documentation, Uses, and more |
| apt-transport-https | lcc, mcc | 1.0 | This APT transport allows the use of repositories accessed via the HTTP Secure protocol (HTTPS), also referred to as HTTP over TLS. It is available by default since apt 1.5 and was available before that in the package apt-transport-https. Note that a transport is never called directly by a user but used by APT tools based on user configuration. | Package Management, Security, Debian, APT | Software Systems Engineering, System Administration | System Utility | Documentation, Uses, and more |
| argweaver | mcc | 1.0 | The ARGweaver software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs). An ARG is a rich data structure for representing the ancestry of DNA sequences undergoing coalescence and recombination. | bioinformatics, genetics, population genetics, software tool | Computational Evolutionary Biology, Bioinformatics | Command-line tool | Documentation, Uses, and more |
| armadillo | lcc | 1.0 | Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab. Description Source: https://arma.sourceforge.net/ |
Linear Algebra, C++ Library | Computer Science, Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| armadillo-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| arpack-devel | lcc | 1.0 | arpack-devel is a subroutine of ARPACK which is a collection of Fortran 77 subroutines designed to solve large scale eigenvalue problems. This package contains the so library links used for building arpack based applications. | Eigenvalue, Numerical Linear Algebra, High-Performance Computing | Applied Mathematics, Numerical Linear Algebra | Library | Documentation, Uses, and more |
| arrayfire | lcc | N/A | Cell ranger tools . | Software Library, Parallel Computing, Gpu Acceleration, Linear Algebra, Signal Processing, Image Processing, Statistics | Parallel Computing, Computer & Information Sciences | Library | Documentation, Uses, and more |
| ase | lcc | 1.0 | ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. Description Source: https://wiki.fysik.dtu.dk/ase/index.html |
Computational Software, Python Library, Molecular Simulations | Chemistry, Other Natural Sciences | Tool | Documentation, Uses, and more |
| assembly-stats | mcc | 1.0 | Assembly-stats is a tool to get assembly statistics from FASTA and FASTQ files. | Genome Assembly, Bioinformatics | Biology, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| astra-toolbox | ecc | N/A | ASTRA Toolbox 2.3.0 installed via Conda environment. | Documentation, Uses, and more | |||
| astral | mcc | 1.0 | ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under the multi-species coalescent model (and thus is useful for handling incomplete lineage sorting, i.e., ILS). ASTRAL finds the species tree that has the maximum number of shared induced quartet trees with the set of gene trees, subject to the constraint that the set of bipartitions in the species tree comes from a predefined set of bipartitions. | Bioinformatics, Phylogenetics | Phylogenomics inference tool | Documentation, Uses, and more | |
| atacseqqc | mcc | 1.0 | Documentation, Uses, and more | ||||
| augustus | lcc | 1.0 | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. Description Source: https://bioinf.uni-greifswald.de/augustus/ |
Gene Prediction, Eukaryotes, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| augustus-braker | lcc | N/A | BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-ES/ET/EP/ETP R14, R15, R17, F1 and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction. | genome annotation, gene prediction, bioinformatics | Bioinformatics | Genome annotation software | Documentation, Uses, and more |
| autoconf | ecc, lcc, mcc | 1.0 | Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. | Build Automation, Software Configuration, Makefiles | General, Engineering & Technology | Build Tools | Documentation, Uses, and more |
| autoconf-archive | ecc | N/A | The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. Description Source: https://github.com/autoconf-archive/autoconf-archive |
General | Service | Documentation, Uses, and more | |
| autodock-vina | mcc | 1.0 | AutoDock Vina is an open-source program for doing molecular docking. AutoDock Vina is one of the docking engines of the AutoDock Suite. | Biology | Application | Documentation, Uses, and more | |
| automake | ecc, lcc, mcc | 1.0 | Automake: GNU Standards-compliant Makefile generator | Build Automation, Software Development, Compilers | General, Engineering & Technology | Compiler | Documentation, Uses, and more |
| autotools | ecc, lcc | N/A | This bundle collect the standard GNU build tools: Autoconf, Automake and libtool | Programming, Software Development, Build Automation | Software Engineering, Systems & Development, Computer & Information Sciences | Build Automation | Documentation, Uses, and more |
| azcopy | mcc | 1.0 | AzCopy is a command-line utility that you can use to copy data to, from, or between storage accounts. This article helps you download AzCopy, connect to your storage account, and then transfer data. | Data Transfer, Cloud Storage, Azure, Command Line Tool | Computer Science, Data Engineering | Command Line Utility | Documentation, Uses, and more |
| bakta | lcc, mcc | 1.0 | Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis. | bacterial genome annotation, prokaryotic genomes, bioinformatics, functional annotation, gene prediction, comparative genomics, sequence analysis | Microbial genomics, Bioinformatics | Genome annotation software | Documentation, Uses, and more |
| bam-readcount | lcc | 1.0 | Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bam-readcount/bam-readcount.html |
Bioinformatics, Genomics, Variant-Calling, Coverage-Assessment | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| bamtools | lcc | 1.0 | BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. Description Source: https://github.com/pezmaster31/bamtools/wiki |
Bioinformatics, Bam Files, Sequence Alignment, Toolkit | Biology, Biological Sciences | Toolkit | Documentation, Uses, and more |
| base | lcc | 1.0 | Documentation, Uses, and more | ||||
| bash | ecc | N/A | Documentation, Uses, and more | ||||
| bayescan | lcc, mcc | 1.0 | BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bayescan/bayescan.html |
Genetic Analysis, Natural Selection, Bayesian Model Comparison | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| bbmap | mcc | 1.0 | Bbmap is a short read aligner, as well as various other bioinformatic tools. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bbmap/bbmap.html |
Bioinformatics, DNA Sequencing, Sequence Alignment | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bbmap_39.08 | mcc | 1.0 | Documentation, Uses, and more | ||||
| bc | ecc | N/A | Documentation, Uses, and more | ||||
| bcbio | mcc | 1.0 | Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. | bioinformatics, genomics, high-throughput sequencing, data analysis | Computational Biology, Bioinformatics | Workflow management software | Documentation, Uses, and more |
| bcftools | lcc, mcc | 1.0 | BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. Description Source: https://samtools.github.io/bcftools/howtos/index.html |
Variant Calling, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcftools-1.11-samtools | lcc | 1.0 | Documentation, Uses, and more | ||||
| bcl2fastq2 | lcc, mcc | 1.0 | Cell ranger tools . | Documentation, Uses, and more | |||
| beagle | mcc | 1.0 | Beagle is is a software package for phasing genotypes and for imputing ungenotyped markers. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/beagle/beagle.html |
Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| beagle-lib | lcc, mcc | 1.0 | BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs. Description Source: https://github.com/beagle-dev/beagle-lib |
Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics | Biology | Library | Documentation, Uses, and more |
| beast | lcc, mcc | 1.0 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Description Source: https://www.beast2.org/ |
Bioinformatics, Computational Biology, Phylogenetics, Molecular Evolution, Bayesian Analysis | Systems Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| beast2 | lcc, mcc | 1.0 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Description Source: https://www.beast2.org/ |
Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference | Ecology, Biological Sciences | Tool | Documentation, Uses, and more |
| beautifulsoup4 | ecc | 1.0 | Beautiful Soup is a library that makes it easy to scrape information from web pages. It sits atop an HTML or XML parser, providing Pythonic idioms for iterating, searching, and modifying the parse tree. | web scraping, HTML parsing, data extraction, Python | Data Science, Web Technologies | Library | Documentation, Uses, and more |
| bedops | lcc, mcc | 1.0 | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Description Source: https://bedops.readthedocs.io/en/latest/ |
Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis | Bioinformatics, Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| bedtools | lcc, mcc | 1.0 | Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. This is an older version of bedtools2. Description Source: https://bedtools.readthedocs.io/en/latest/ |
Bioinformatics, Genomics, Data Analysis, Tool | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| berkeley-db | ecc | N/A | Berkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications. Description Source: https://docs.oracle.com/database/bdb181/ |
Storage, Hpc Applications | Library | Documentation, Uses, and more | |
| binutils | lcc | N/A | binutils: GNU binary utilities | Binary Tools, Linker, Assembler, Object Files | General, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| bioawk | mcc | 1.0 | Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. \r Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bioawk/bioawk.html |
Bioinformatics, Data Processing, File Formats, Data Analysis | Bioinformatics, Biological Sciences | Scripting Tool | Documentation, Uses, and more |
| biobakery_workflows | lcc | 1.0 | bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. | bioinformatics, microbiome, data analysis, workflow | Computational Biology, Bioinformatics | Workflow Management | Documentation, Uses, and more |
| biocmanager | lcc | 1.0 | BiocManager is an R package that streamlines access to the Bioconductor ecosystem by providing reliable tools for installing, updating, and managing bioinformatics packages. It ensures that users retrieve versions compatible with their R installation, maintaining consistency and reproducibility across workflows. BiocManager also simplifies dependency resolution across both Bioconductor and CRAN, making it easier to build and maintain complex analysis environments. | R, Bioconductor, Package Management | Computational Biology, Genomics | Package Manager | Documentation, Uses, and more |
| bioconda | lcc, mcc | 1.0 | Bioconda is a specialized Conda channel that provides thousands of pre-built bioinformatics software packages, enabling fast, consistent, and reproducible installation across platforms. It streamlines software management for life-science research by simplifying dependencies and environment setup. | bioinformatics, conda, package management, software distribution | Bioinformatics, Genomics | Package Manager | Documentation, Uses, and more |
| bioconda::mummer4=4.0.1 | lcc | 1.0 | Documentation, Uses, and more | ||||
| bioconductor-atacseqqc | mcc | 1.0 | ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. | ATAC-seq, Bioinformatics, Quality Control | Molecular Biology, Bioinformatics | Quality Control Tool | Documentation, Uses, and more |
| bioconductor-champ | lcc | N/A | The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations. | Bioinformatics, Genomics, R | Bioinformatics, Molecular Biology | R Package | Documentation, Uses, and more |
| bioconductor-deseq2 | lcc | N/A | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | RNA-Seq, Differential Expression, Bioconductor, Genomics, Statistics | Genomics, Molecular Biology | R Package | Documentation, Uses, and more |
| bioconductor-dss | lcc | 1.0 | DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | bioinformatics ,methylation, genomics, Bioconductor | Bioinformatics, Molecular Biology | R package | Documentation, Uses, and more |
| bioconductor-edger | lcc | N/A | Differential expression analysis of sequence count data. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models, quasi-likelihood, and gene set enrichment. Can perform differential analyses of any type of omics data that produces read counts, including RNA-seq, ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE, CAGE, metabolomics, or proteomics spectral counts. RNA-seq analyses can be conducted at the gene or isoform level, and tests can be conducted for differential exon or transcript usage. | RNA-Seq, Differential Expression, Bioconductor, Statistics | Computational Biology, Bioinformatics | Statistical Analysis | Documentation, Uses, and more |
| bioconductor-lea | mcc | 1.0 | Documentation, Uses, and more | ||||
| bioconductor-maftools | mcc | 1.0 | Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort. | bioinformatics, cancer genomics, R package, data visualization | Cancer Research, Bioinformatics | R package | Documentation, Uses, and more |
| bionano | mcc | 1.0 | bionano OGM solutions provide the essential tools clinicians and researchers need to reveal actionable insights from all classes of genomic variations | structural variation, genome assembly, optical mapping | Molecular Biology, Life Sciences | Bioinformatics Software | Documentation, Uses, and more |
| biopython | lcc, mcc | 1.0 | Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Description Source: https://biopython.org/ |
Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| bis-snp | mcc | 1.0 | BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. | bisulfite sequencing, DNA methylation, SNP calling, epigenomics, bioinformatics, NGS analysis | Epigenomics, Bioinformatics | Variant and DNA methylation analysis software | Documentation, Uses, and more |
| bismark | lcc, mcc | 1.0 | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. Description Source: https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics | Genomics, Biological Sciences | Alignment & Methylation Analysis | Documentation, Uses, and more |
| bison | lcc | N/A | Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. | Parser Generator, Programming Language Tool | General, Computer & Information Sciences | Parser Generator | Documentation, Uses, and more |
| blasr | lcc, mcc | 1.0 | Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blasr/blasr.html |
Alignment, Sequencing, Genomics | Biology, Biological Sciences | Mapping | Documentation, Uses, and more |
| blast | lcc, mcc | 1.0 | BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blast/blast.html |
Bioinformatics, Sequence Alignment, Homology Search | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| blat | lcc | N/A | BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. Description Source: https://genome.ucsc.edu/cgi-bin/hgBlat |
Sequence Analysis, DNA Alignment, Genomic Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| blobtoolkit | mcc | 1.0 | Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering. | genomics, bioinformatics, data visualization, software tools | Computational Biology, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| blobtools | mcc | 1.0 | Blobtools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blobtools/blobtools.html |
Genome Assembly, Data Visualization, Metagenomics | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| blobtools_v1.1.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| bonito | lcc | N/A | Bonito is an open source research basecaller for Oxford Nanopore reads. | bioinformatics, nanopore sequencing, basecalling, deep learning | Bioinformatics | Documentation, Uses, and more | |
| boost | lcc | N/A | Boost free peer-reviewed portable C++ source libraries | C++ Libraries, Programming Support, Efficiency Enhancement | Computer Science, Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| boost-devel | mcc | 1.0 | The Boost.MPL library is a general-purpose, high-level C++ template metaprogramming framework of compile-time algorithms, sequences and metafunctions. It provides a conceptual foundation and an extensive set of powerful and coherent tools that make doing explict metaprogramming in C++ as easy and enjoyable as possible within the current language. | c++, generic programming, system utilities, Libraries | Systems Programming, Computer Science | Library | Documentation, Uses, and more |
| bowtie | lcc, mcc | 1.0 | Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. Description Source: https://bowtie-bio.sourceforge.net/manual.shtml |
Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| bowtie2 | lcc, mcc | 1.0 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning to relatively long (e.g. mammalian) genomes. Description Source: https://github.com/BenLangmead/bowtie3 |
Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Sequence Alignment | Documentation, Uses, and more |
| bpp | lcc | N/A | BPP is a Bayesian Markov chain Monte Carlo (MCMC) program for analyzing sequence alignments from multiple loci and multiple closely-related species under the multispecies coalescent (MSC) model. BPP takes into account episodic and continuous gene flow through its implementation of the multispecies coalescent with introgression (MSC-I) model for episodic events, and the multispecies coalescent with migration (MSC-M) model for continuous interactions. | phylogenetics, molecular evolution, comparative genomics | Evolutionary Biology, Life Sciences | Statistical Software | Documentation, Uses, and more |
| braker | lcc | 1.0 | Documentation, Uses, and more | ||||
| braker3 | mcc | 1.0 | Documentation, Uses, and more | ||||
| breakdancer | lcc, mcc | 1.0 | a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs. | genomics, bioinformatics, structural variants, next-generation sequencing | Genomic Analysis, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| bsbolt | lcc | 1.0 | a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation. | bisulfite sequencing, DNA methylation, read alignment, variant calling, epigenomics, bioinformatics | Epigenomics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| build-essential | lcc, mcc | 1.0 | build-essential is a foundational Linux package that bundles the minimal compiler, linker, and build tools needed to turn source code into executable programs. It serves as a standard baseline for software development environments, ensuring that common C and C++ projects can be built reliably from source. | compiler toolchain, software compilation, development utilities | Software Engineering, Open Source Development | Package | Documentation, Uses, and more |
| burai | lcc | N/A | Burai is a graphical user interface (GUI) designed to simplify running and managing Quantum ESPRESSO calculations for materials science and computational physics. It allows users to set up input files, execute simulations, and visualize results without needing to work directly with complex command-line workflows. | quantum espresso, density functional theory, materials simulation | Computational Physics, Physical Sciences | Scientific Application | Documentation, Uses, and more |
| busco | lcc, mcc | 1.0 | Benchmarking Universal Single-Copy Orthologs (BUSCO) is used for assessing genome assembly and annotation completeness. Description Source: https://gitlab.com/ezlab/busco |
Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs | Bioinformatics, Biological Sciences | Tools | Documentation, Uses, and more |
| bwa | lcc, mcc | 1.0 | BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. Description Source: https://bio-bwa.sourceforge.net/ |
Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs) | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bwa-mem2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| bwakit | mcc | 1.0 | Documentation, Uses, and more | ||||
| bwameth | mcc | 1.0 | Bwameth is a tool for fast and accurante alignment of BS-Seq reads. Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bwameth/bwameth.html |
DNA Methylation, Bisulfite Sequencing, Alignment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bx-python | mcc | 1.0 | Documentation, Uses, and more | ||||
| bzip2 | ecc, lcc, mcc | 1.0 | bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. | File Compression, Data Compression, Utility Software | General, Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| bzip2-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| bzip2-libs | mcc | 1.0 | Documentation, Uses, and more | ||||
| ca-certificates-mozilla | ecc | N/A | Documentation, Uses, and more | ||||
| cactus | lcc | 1.0 | Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. Description Source = https://github.com/ComparativeGenomicsToolkit/cactus?tab=readme-ov-file | Computational Software, Hpc Tools | Gravitational Physics, Physical Sciences | Simulation Software | Documentation, Uses, and more |
| canu | lcc, mcc | 1.0 | canu software. | Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics | Genomics, Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| canu-2.2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| ccl | ecc, lcc | N/A | CCL (Cpp Command Line Library) is a C++ library targeting Unix platform that makes it easy to define and parse command line arguments. It provides a simple and intuitive way to define and parse command-line arguments for C++ programs. | Command Line Interface, C++ Library | Documentation, Uses, and more | ||
| cd-hit | lcc, mcc | 1.0 | Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences. | Sequence Analysis, Clustering, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| cd-hit-auxtools | lcc | 1.0 | Documentation, Uses, and more | ||||
| cdbfasta | lcc | 1.0 | Documentation, Uses, and more | ||||
| cdhit | lcc | 1.0 | Documentation, Uses, and more | ||||
| cdna_cupcake | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| cellbender | mcc | 1.0 | Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. | Single-Cell RNA-Seq, Data Processing, Denoising, Batch Effects, Bioinformatics | Genetics, Biological Sciences | Python Library | Documentation, Uses, and more |
| cellranger | lcc, mcc | 1.0 | Cell ranger tools . | Bioinformatics, Single-Cell RNA-Seq, Data Analysis | Biology, Biological Sciences | Documentation, Uses, and more | |
| cellranger-arc | lcc | N/A | Cell ranger arc tools . | Single-Cell Analysis, Chromatin Accessibility, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cellranger-atac | lcc | N/A | Cell ranger arc tools . | Biology | Application | Documentation, Uses, and more | |
| cgmaptools | lcc | 1.0 | Documentation, Uses, and more | ||||
| charliecloud | lcc | N/A | Lightweight user-defined software stacks for high-performance computing | Containerization, Software Development, Research Tools | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| charmm | lcc | N/A | Documentation, Uses, and more | ||||
| checkm-genome | lcc, mcc | 1.0 | Checkm-genome provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. | Metagenomics, Microbial Ecology, Genome Quality Assessment | Environmental Biology, Biological Sciences | Genome Quality Assessment Tool | Documentation, Uses, and more |
| checkm2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| checkv | mcc | 1.0 | Documentation, Uses, and more | ||||
| chemshell | lcc | N/A | canu software. | Documentation, Uses, and more | |||
| chewbbaca | lcc | 1.0 | chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. | Whole-Genome Analysis, Microbial Genotyping, Bacterial Typing, Phylogenetic Inference, Bioinformatics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| chopper | mcc | 1.0 | Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python. | Bioinformatics, Ngs Data Analysis, Sequence Trimming, High-Throughput Sequencing | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ciao | lcc | N/A | Documentation, Uses, and more | ||||
| circos | lcc | N/A | Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Description Source: https://circos.ca/ |
Data Visualization, Genomics, Biological Sciences, Circular Layout | Bioinformatics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| citcoms | lcc | N/A | CitcomS is a parallel finite-element simulation software used to model mantle convection and other large-scale geodynamic processes within the Earth. It is designed for high-performance computing environments and allows researchers to study thermal and compositional evolution of the mantle in spherical or regional geometries. | mantle convection, finite-element modeling, high-performance computing | Geodynamics, Earth Sciences | Simulation Software | Documentation, Uses, and more |
| clck | lcc | N/A | Documentation, Uses, and more | ||||
| clinfo | lcc | 1.0 | Documentation, Uses, and more | ||||
| clumpp | mcc | 1.0 | CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. | population structure, clustering alignment, genetic analysis | Life Sciences, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| clumpp_linux64.1.1.2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| clust | mcc | 1.0 | Clust is a fully automated method for identification of clusters (groups) of genes that are consistently co-expressed (well-correlated) in one or more heterogeneous datasets from one or multiple species. | Clustering, Time Series Data, Pattern Identification | Other Computer & Information Sciences | Data Analysis Tool | Documentation, Uses, and more |
| cmake | ecc, lcc, mcc | 1.0 | CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. | Build System, Cross-Platform, Software Development | Software Engineering, Systems & Development, Engineering & Technology | Developer Tools | Documentation, Uses, and more |
| cmake3 | lcc | 1.0 | Documentation, Uses, and more | ||||
| cmdstanr 0.5.2 and opencl | lcc | 1.0 | Documentation, Uses, and more | ||||
| cogent | mcc | 1.0 | Cogent NGS Discovery Software (CogentDS) is bioinformatic software for user-friendly analysis of sequencing data generated with Takara Bio platforms. The Cogent NGS Analysis Pipeline (CogentAP) can be used to prepare files ready for import into CogentDS. | long-read sequencing, transcript reconstruction, isoform analysis | Life Sciences, Bioinformatics | Analysis Tool | Documentation, Uses, and more |
| colabfold | lcc | N/A | ColabFold is a web-based tool that leverages artificial intelligence to predict protein structures rapidly and accurately, making cutting-edge protein folding accessible to researchers without requiring extensive computational resources. It builds on the technology of AlphaFold by DeepMind, providing a user-friendly platform for scientific exploration and discovery in the field of bioinformatics and structural biology. | Protein Structure Prediction, Deep Learning, Biophysical Modeling | Bioinformatics, Biological Sciences | Protein Structure Prediction Tool | Documentation, Uses, and more |
| compiler | ecc, lcc | N/A | A compiler is a special program that processes statements written in a particular programming language and turns them into machine language or "code" that a computer's processor uses. It typically acts as a translator that converts high-level programming languages into machine language. | Compiler, Software Development, Programming | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| compiler-intel-llvm | ecc | N/A | LLVM is a free and open source compiler infrastructure originally built for C and C++. Although its name initially stood for low-level virtual machine, LLVM is now a technology that deals with much more than just virtual machines. The name is no longer officially an initialism. | llvm, high-performance computing, intel optimization | High Performance Computing, Software Engineering | Compiler | Documentation, Uses, and more |
| compiler-rt | ecc, lcc | N/A | builtins - low-level target-specific hooks required by code generation and other runtime components sanitizer runtimes - AddressSanitizer, ThreadSanitizer, UndefinedBehaviorSanitizer, MemorySanitizer, LeakSanitizer, DataFlowSanitizer profile - library which is used to collect coverage information BlocksRuntime - target-independent implementation of Apple "Blocks" runtime interfaces Description Source: https://github.com/conda-forge/compiler-rt-feedstock/blob/main/recipe/meta.yaml | Runtime Library, Compiler Support, Low-Level Support, Language Features | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| compiler-rt32 | lcc | N/A | The compiler-rt32 project is a runtime library that provides functionality for compilers in the 32-bit architecture. It includes various runtime components such as sanitizers, builtins, and support libraries for handling memory operations and error detection. | Compiler, Runtime Library, 32-Bit Architecture | Computer Science, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| compiler32 | lcc | N/A | compiler32 is a lightweight and efficient compiler software designed for compiling source code into executable programs. It supports various programming languages and optimization techniques to enhance the performance of the compiled code. | Compiler, Software Development, Programming | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| compleasm | mcc | 1.0 | Compleasm is a bioinformatics tool for assessing the completeness of genome assemblies using conserved single-copy orthologs. It provides a fast, lightweight alternative to BUSCO for evaluating genome quality, particularly in large-scale or high-throughput assembly workflows. | genome completeness, assembly evaluation, ortholog analysis | Computational genomics, Bioinformatics | Computational Biology Tool | Documentation, Uses, and more |
| comsol | lcc | N/A | COMSOL is an advanced simulation software that provides a finite element analysis, solver, and multiphysics simulation capabilities. It allows for the modeling of complex engineering and scientific problems involving coupled phenomena across fields like electromagnetics, mechanics, fluid dynamics, and chemical engineering, offering a versatile platform for both research and industrial applications. | Simulation, Modeling, Physics, Engineering, Optimization | Engineering & Technology | Simulation Software | Documentation, Uses, and more |
| conda | lcc | N/A | R | Documentation, Uses, and more | |||
| conda-forge | ecc, lcc, mcc | 1.0 | conda-forge is a community effort and a GitHub organization which contains repositories of conda recipes and thus provides conda packages for a wide range of software. The built distributions are uploaded to anaconda.org/conda-forge and can be installed with conda. | package management,conda,open source,community | Scientific Computing Infrastructure, Data Science | Software Distribution Platform | Documentation, Uses, and more |
| conda-libmamba-solver | lcc | 1.0 | conda-libmamba-solver is a new solver for the conda package manager which uses the solver from the mamba project behind the scenes, while carefully implementing conda's functionality and expected behaviors on top. The library used by mamba to do the heavy-lifting is called libsolv. | package management, dependency resolution, conda, libmamba | Software Engineering, Computer Science | Dependency Solver | Documentation, Uses, and more |
| conmon | ecc | N/A | Documentation, Uses, and more | ||||
| cortex_con | mcc | 1.0 | Documentation, Uses, and more | ||||
| cortexassembler | lcc | N/A | assembler software. | Documentation, Uses, and more | |||
| coseg | mcc | 1.0 | This program is derived from three C programs and several perl scripts written by Alkes Price as part of an analysis of Alu elements in the human genome. The program was first adapted for use with other repeat families and then extended to support consideration of three co-segregating mutations using Alkes statistical model. In 2008 with the help of Andy Siegel an alternative statistical model was developed and the codebase repackaged into the single source file. | co-segregation analysis, genomics, genetic variation, population genetics, comparative genomics, bioinformatics | Population Genetics, Bioinformatics | Bioinformatics analysis tool | Documentation, Uses, and more |
| coverm | mcc | 1.0 | Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. | Metagenomics, Bioinformatics, Genomics | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| cp2k | lcc, mcc | 1.0 | CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. Description Source: https://www.cp2k.org/ |
Computational Chemistry, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Molecular Simulation | Documentation, Uses, and more |
| cpanminus | lcc, mcc | 1.0 | cpanminus is a script to get, unpack, build and install modules from CPAN and does nothing else.\r It's dependency free (can bootstrap itself), requires zero configuration, and stands alone. When running, it requires only 10MB of RAM. |
Perl, CPAN, package management, dependency installation, command-line tool, developer tooling | Software Engineering, Computer Science | Package Manager | Documentation, Uses, and more |
| crackling | ecc, lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| crossmap | lcc | N/A | Crossmap is a program for genome coordinates conversion between different assemblies. | Genome Assembly, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cuda | lcc | 1.0 | Nvidia CUDA toolkit and samples | Parallel Computing, Gpu Programming, High Performance Computing, Software Development | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| cudnn | lcc | 1.0 | Nvidia cudNN library | Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Accelerator | Documentation, Uses, and more |
| cufflinks | lcc, mcc | 1.0 | Cufflinks software. | RNA-Seq, Transcriptomics, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| curl | ecc, lcc, mcc | 1.0 | libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. | Networking, Data Transfer, Command-Line, Scripting | Computer & Information Sciences, Other Computer & Information Sciences | Networking Tool | Documentation, Uses, and more |
| cutadapt | lcc, mcc | 1.0 | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads. Description Source: https://cutadapt.readthedocs.io/en/stable/ |
Bioinformatics, Ngs, Sequence Analysis, Genomics | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| cython | lcc, mcc | 1.0 | Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself. Description Source: https://cython.org/ |
Programming Language, C Extensions, Python, Cython | Computer & Information Sciences | Language Compiler | Documentation, Uses, and more |
| dakota | lcc | N/A | Documentation, Uses, and more | ||||
| dal | lcc | N/A | DAL is a library for collision avoidance in robotics applications. | Robotics, Collision Avoidance | Engineering & Technology | Collision Avoidance Software | Documentation, Uses, and more |
| dask | lcc | 1.0 | Dask makes it easy to scale the Python libraries that you know and love like NumPy, pandas, and scikit-learn. It also allows you to Parallelize any Python code with Dask Futures, letting you scale any function and for loop, and giving you control and power in any situation. Description Source: https://www.dask.org/ |
Parallel Computing, Scalable Computing, Analytics, Data Science | Computer & Information Sciences | Library | Documentation, Uses, and more |
| datasets | ecc | 1.0 | Datasets is a lightweight library providing one-line dataloaders for many public datasets and one liners to download and pre-process any of the number of datasets major public datasets provided on the HuggingFace Datasets Hub. Datasets are ready to use in a dataloader for training/evaluating a ML model (Numpy/Pandas/PyTorch/TensorFlow/JAX). Datasets also provide an API for simple, fast, and reproducible data pre-processing for the above public datasets as well as your own local datasets in CSV/JSON/text. Description Source: https://github.com/conda-forge/datasets-feedstock/blob/main/recipe/meta.yaml | Data, Research, Analysis, Processing, Sharing | Documentation, Uses, and more | ||
| debugger | ecc, lcc | N/A | Intel® oneAPI Application Debugger (gdb-oneapi) | Debugging, Software Development | Engineering & Technology | Debugger | Documentation, Uses, and more |
| deep-md-cpu | lcc | N/A | DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning-based models of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. | Deep Learning,Molecular Dynamics,Computational Chemistry | Chemistry, Computational Science | Library | Documentation, Uses, and more |
| deep-md-gpu | lcc | N/A | Documentation, Uses, and more | ||||
| deepchem | lcc | 1.0 | DeepChem is a Python library for machine learning and deep learning on molecular and quantum datasets. It is built on top of PyTorch, and other popular ML frameworks. It is designed to make it easy to apply ML to new domains, and to build and benchmark new models. It is also designed to make it easy to use ML in production, by providing easy-to-use model export and deployment APIs. | deep learning, cheminformatics, drug discovery | Chemoinformatics, Drug Discovery | Library | Documentation, Uses, and more |
| deepchem-2.5.0-gpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| deeppolisher | mcc | 1.0 | DeepPolisher is a transformer-based sequencing correction method similar to DeepConsensus. DeepPolisher is designed to identify errors in genome assemblies. DeepPolisher takes haplotype-specific reads aligned to phased assemblies and produces a VCF file containing potential errors in the assembly. Currently, DeepPolisher can take PacBio HiFi-based assemblies and read alignments to identify potential errors. | genome polishing, long-read sequencing, deep learning, neural networks, genome assembly, error correction, bioinformatics | Genome Assembly, Bioinformatics | Analysis software | Documentation, Uses, and more |
| deeptools | lcc, mcc | 1.0 | deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Description Source: https://deeptools.readthedocs.io/en/latest/ |
Bioinformatics, Hpc Tools, Computational Software | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| deepvariant | lcc, mcc | 1.0 | DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. | Variant Calling, Genetic Variants, Deep Learning, DNA Sequencing | Genomics, Biological Sciences | Variant Caller | Documentation, Uses, and more |
| default-jdk | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| default-jre | mcc | 1.0 | Documentation, Uses, and more | ||||
| delly | lcc | 1.0 | Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. | Structural Variant Discovery, Sv Detection, Genomics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| detonate | lcc | 1.0 | Documentation, Uses, and more | ||||
| dev-utilities | ecc, lcc | N/A | Sample headers and CLI sample browser (oneapi-cli). | Development, Utilities | Computer & Information Sciences, Other Computer & Information Sciences | Tools | Documentation, Uses, and more |
| diamond | lcc, mcc | 1.0 | diamond software. | Sequence Alignment, Ngs Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| diamond-linux64 | mcc | 1.0 | Documentation, Uses, and more | ||||
| diffutils | ecc, lcc | 1.0 | GNU Diffutils is a package of several programs related to finding differences between files. Description Source: https://github.com/conda-forge/diffutils-feedstock/blob/main/recipe/meta.yaml | Text Comparison, File Difference, Text Analysis, Version Control | Engineering & Technology | Text Processing | Documentation, Uses, and more |
| dimemas | lcc | N/A | Dimemas tool | Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems | Engineering & Technology | Performance Prediction Tool | Documentation, Uses, and more |
| dispy | lcc | N/A | dispy is a generic, comprehensive, yet easy to use framework and tools for creating, using and managing compute clusters to execute computations in parallel across multiple processors in a single machine (SMP), among many machines in a cluster, grid or cloud. | distributed computing, parallel processing, Python, task scheduling, cluster computing, HPC | High Performance Computing, Computer Science | Library | Documentation, Uses, and more |
| dnf-plugins-core | mcc | 1.0 | Core plugins to use with DNF package manager. | DNF, RPM, Linux, package management, system administration, repository management, plugins | Software Engineering, Computer Science | Package Manager | Documentation, Uses, and more |
| dnnl | ecc, lcc | N/A | Performance library of basic building blocks for deep learning applications | Deep Learning, Neural Networks, Machine Learning, Performance Optimization | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| dnnl-cpu-gomp | lcc | N/A | The dnnl-cpu-gomp is an open-source deep neural network library developed for CPU-based computations employing OpenMP (Open Multi-Processing) as a thread-processing technology. | Deep Learning, Neural Networks, Openmp, Cpu Computing | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| dnnl-cpu-iomp | lcc | N/A | dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance. | Deep Learning, Optimization, Cpu Acceleration | Computer & Information Sciences | Documentation, Uses, and more | |
| dnnl-cpu-tbb | lcc | N/A | Documentation, Uses, and more | ||||
| dock6 | lcc | N/A | DOCK 6 is written in C++ and is functionally separated into independent components, allowing a high degree of program flexibility. Accessory programs are written in C and Fortran 77. We provide source code for all programs. The DOCK suite of programs has modest disk space and memory requirements. | molecular docking, virtual screening, drug discovery, protein–ligand interactions, computational chemistry, structure-based design | Chemistry, Computational Chemistry | Scientific Software | Documentation, Uses, and more |
| dorado | lcc, mcc | 1.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. Description Source: https://github.com/nanoporetech/dorado |
Performance Evaluation, Benchmarking, Hpc, Supercomputing | Biology, Engineering & Technology | Tool | Documentation, Uses, and more |
| dorodo | mcc | 1.0 | Documentation, Uses, and more | ||||
| dos2unix | lcc | 1.0 | dos2unix converts text files with DOS or Mac line breaks to Unix line breaks and vice versa. Description Source: https://dos2unix.sourceforge.io/#DOS2UNIX |
Text Conversion, Line Endings, Command-Line Utility | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| doxygen | lcc | N/A | Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. | Documentation Generator, Software Development, Programming | Software Engineering, Systems & Development | Tool | Documentation, Uses, and more |
| dpct | ecc, lcc | N/A | Migrate existing CUDA* code to SYCL code. | Cuda Programming, Gpu Computing, Parallel Programming | Computer & Information Sciences | Development Compiler | Documentation, Uses, and more |
| dpl | ecc, lcc | N/A | Intel(R) oneAPI DPC++ Library provides an alternative for C++ developers who create heterogeneous applications and solutions. Its APIs are based on familiar standards - C++ STL, Parallel STL (PSTL), Boost.Compute, and SYCL* - to maximize productivity and performance across CPUs, GPUs, and FPGAs. | Programming Language Analysis, Syntax Analysis, Language Structure Analysis | Documentation, Uses, and more | ||
| dplyr | lcc | 1.0 | dplyr is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges | Data Manipulation,R,Data Science,Statistics | Statistics, Data Analysis | Library | Documentation, Uses, and more |
| drep | mcc | 1.0 | Drep is a python program for rapidly comparing large numbers of genomes. | Microbiome, Genome Analysis, Bioinformatics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| dsuite | lcc, mcc | 1.0 | Dsuite provides a fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species. Description Source: https://github.com/millanek/Dsuite |
Python Library, Data Analysis, Data Visualization | Biostatistics, Statistics & Probability | Python Library | Documentation, Uses, and more |
| dvipng | lcc | 1.0 | This program makes PNG and/or GIF graphics from DVI files as obtained from TeX and its relatives. | LaTeX, TeX, DVI, PNG, document rendering, command-line utility, typesetting | Computational Publishing, Computer Science | Document processing utility | Documentation, Uses, and more |
| e2fsprogs | ecc | N/A | Documentation, Uses, and more | ||||
| eagle_v2.4.1 | mcc | 1.0 | The Eagle software estimates haplotype phase [1] either within a genotyped cohort or using a phased reference panel. | haplotype phasing, genotype data, population genetics, GWAS, imputation preprocessing, large-scale genomics | Population Genetics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| eaglev | mcc | 1.0 | Documentation, Uses, and more | ||||
| earlgrey | mcc | 1.0 | With the EarlGrey framework, you have access to enhanced synchronization features. EarlGrey automatically synchronizes with the UI, network requests, and various queues; but still allows you to manually implement customized timings, if needed. | General Tags transposable elements, repeat annotation, genome annotation, de novo TE discovery, eukaryotic genomes, bioinformatics pipeline | Evolutionary Genomics, Bioinformatics | Analysis software | Documentation, Uses, and more |
| easybuild | ecc, lcc | N/A | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. | Software Building, High-Performance Computing, Automation | Engineering & Technology | Build Automation | Documentation, Uses, and more |
| ecc/cuda | ecc | N/A | NVIDIA CUDA Toolkit 12.8.0 installed at /share/apps/cuda/12.8.0_570.86.10 | Documentation, Uses, and more | |||
| ecc/miniconda3 | ecc | N/A | Miniconda is a minimal installer for conda, a package manager and environment manager. | Documentation, Uses, and more | |||
| ecc/rclone | ecc | N/A | Rclone is a command-line tool for syncing files to and from cloud storage. | Documentation, Uses, and more | |||
| ecc/spack | ecc | N/A | Spack 0.23.1 is a flexible package manager for HPC environments. | Documentation, Uses, and more | |||
| ed | ecc | N/A | Documentation, Uses, and more | ||||
| eggnog-mapper | mcc | 1.0 | Eggnog-mapper is a tool for fast functional annotation of novel sequences. | Functional Annotation, Orthology, Gene Function Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| eigen | lcc | N/A | eigen free peer-reviewed portable C++ source libraries | Linear Algebra, Numerical Computation, C++ Library | Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| elfutils | ecc | N/A | elfutils is a collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux. Description Source: https://sourceware.org/elfutils/ |
Binary Tool, Elf Files, Debugging, Programming | Documentation, Uses, and more | ||
| em | lcc | N/A | Documentation, Uses, and more | ||||
| emboss | lcc | 1.0 | R is a language and environment for statistical computing and graphics (S-Plus like). | Bioinformatics, Computational Biology, Sequence Analysis, Biological Data | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| ensembl-vep | lcc, mcc | 1.0 | VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Description Source: https://useast.ensembl.org/info/docs/tools/vep/index.html |
Biology | Documentation, Uses, and more | ||
| ensembletr | mcc | 1.0 | EnsembleTR is a tool for ensemble Tandem Repeat (TR) calling. It takes one or more VCF files with TR genotypes for a panel of samples and outputs a consensus set of genotypes. | transcriptomics, RNA-seq, ensemble methods, gene expression, transcript reconstruction, bioinformatics | RNA Sequencing Analysis, Bioinformatics | Analysis software | Documentation, Uses, and more |
| entap | mcc | 1.0 | The Eukaryotic Non-Model Transcriptome Annotation Pipeline (EnTAP) is designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes. | transcriptome annotation, non-model organisms, functional annotation, ortholog identification, RNA-seq, bioinformatics pipeline | Genome Automation, Bioinformatics | Analysis software | Documentation, Uses, and more |
| epel-release | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| exabayes | lcc | N/A | ExaBayes is a software package used for Bayesian inference of phylogenetic trees and parameters. | Bayesian Inference, Phylogenetics, Parallel Computing, Mcmc, Hpc | Ecology, Biological Sciences | Phylogenetic Software | Documentation, Uses, and more |
| excerpt | mcc | 1.0 | The extra-cellular RNA processing toolkit (exceRpt) was designed to handle the variable contamination and often poor quality data obtained from low input smallRNA-seq samples such as those obtained from extra-cellular preparations. | text processing, field extraction, command-line, Unix utilities, shell pipelines, data wrangling | Software Utilities, Computer Science | Command-line utility | Documentation, Uses, and more |
| exonerate | lcc | 1.0 | Genomic software . | Sequence Alignment, Homology Search, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| expat | ecc, lcc | N/A | Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) | Xml Parser, Library | Computer & Information Sciences | Xml Parser | Documentation, Uses, and more |
| extrae | lcc | N/A | Extrae tool | Performance Analysis, Trace Data, Parallel Applications, Distributed Applications | Computer & Information Sciences, Software Engineering, Systems & Development, Engineering & Technology, Training, Infrastructure & Instrumentation | Tool | Documentation, Uses, and more |
| fast5 | lcc | 1.0 | Documentation, Uses, and more | ||||
| fastani | lcc, mcc | 1.0 | FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Description Source: https://github.com/ParBLiSS/FastANI |
Bioinformatics, Genome Comparison, Bacterial Genomes | Biology, Biological Sciences | Genome Analysis Tool | Documentation, Uses, and more |
| fastp | lcc, mcc | 1.0 | Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc). | Bioinformatics, Sequencing, Data Processing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| fastqc | lcc | 1.0 | FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. Whereas Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems which were generated by the sequencer itself. Description Source: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/1%20Introduction/1.1%20What%20is%20FastQC.html |
Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| faststructure | mcc | 1.0 | fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. | Population Genetics, Structural Biology, Genomics | Genetics, Biological Sciences | Inference Tool | Documentation, Uses, and more |
| fastx_toolkit | lcc, mcc | 1.0 | The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Description Source: http://hannonlab.cshl.edu/fastx_toolkit/ |
Bioinformatics, Short-Reads, Preprocessing | Biology, Biological Sciences | Pre-Processing Tool | Documentation, Uses, and more |
| feems | lcc | 1.0 | Documentation, Uses, and more | ||||
| fenics | lcc | N/A | FEniCS is a popular open-source computing platform for solving partial differential equations (PDEs) with the finite element method (FEM). FEniCS enables users to quickly translate scientific models into efficient finite element code. | partial differential equations, finite element method, numerical simulation, scientific computing, Python, C++ | Computational Mathematics, Computational Science | Scientific computing software | Documentation, Uses, and more |
| fenicsx | mcc | 1.0 | Documentation, Uses, and more | ||||
| ffmpeg | mcc | 1.0 | FFmpeg is a collection of libraries and tools to process multimedia content such as audio, video, subtitles and related metadata. Description Source: https://github.com/FFmpeg/FFmpeg |
Media Processing, Multimedia, Video, Audio | Engineering & Technology | Tool | Documentation, Uses, and more |
| fftw | lcc | N/A | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. | Signal Processing, Data Compression, Partial Differential Equations | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| file | lcc | 1.0 | The file command is "a file type guesser", that is, a command-line tool that tells you in words what kind of data a file contains. Description Source: https://www.darwinsys.com/file/ |
File Management, Command-Line Utility | Command Line Tool | Documentation, Uses, and more | |
| filtlong | mcc | 1.0 | Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. | Bioinformatics, Long Read Sequencing, Sequence Data Processing | Biological Sciences | Data Filtering Tool | Documentation, Uses, and more |
| finder | lcc | 1.0 | Finder software. | Documentation, Uses, and more | |||
| finder_v1.1.0 | lcc | 1.0 | Documentation, Uses, and more | ||||
| findutils | ecc, lcc | 1.0 | The GNU Find Utilities are the basic directory searching utilities of the GNU operating system. These programs are typically used in conjunction with other programs to provide modular and powerful directory search and file locating capabilities to other commands. | Unix, Linux, file searching, command-line tools, system utilities, shell scripting | Systems Programming, Computer Science | System utility software | Documentation, Uses, and more |
| finestructure | mcc | 1.0 | Documentation, Uses, and more | ||||
| flash | mcc | 1.0 | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. Description Source: https://ccb.jhu.edu/software/FLASH/ |
Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis | Physical Sciences | Computational Physics | Documentation, Uses, and more |
| flex | lcc | N/A | Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. | Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator | Documentation, Uses, and more | ||
| fluent | lcc | N/A | Documentation, Uses, and more | ||||
| flye | lcc, mcc | 1.0 | Flye: Fast and accurate de novo assembler for single molecule sequencing reads | Genome Assembly, Long-Read Sequencing, Nanopore Sequencing | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| foss | lcc | N/A | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. | Free Software, Open Source Software, Software Development | Other Computer & Information Sciences | Software Library | Documentation, Uses, and more |
| fpa | mcc | 1.0 | Documentation, Uses, and more | ||||
| fragpipe | mcc | 1.0 | Documentation, Uses, and more | ||||
| freebayes | lcc, mcc | 1.0 | Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. | Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| freeglut3-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| funannotate | mcc | 1.0 | Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. Description Source: https://funannotate.readthedocs.io/en/latest/# |
Genome Prediction, Genome Annotation, Fungi, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| fuse-overlayfs | ecc | N/A | Documentation, Uses, and more | ||||
| galba | mcc | 1.0 | Documentation, Uses, and more | ||||
| gamess | lcc | N/A | GAMESS | Quantum Chemistry, Electronic Structure Calculations, Ab Initio Calculations | Physical Sciences, Chemical Sciences | Quantum Chemistry | Documentation, Uses, and more |
| gangstr | mcc | 1.0 | GangSTR is a tool for genome-wide profiling tandem repeats from short reads. | Str, Genotyping, Short Tandem Repeats, Sequencing Data Analysis | Genomics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| gapless | mcc | 1.0 | Documentation, Uses, and more | ||||
| gapless-0.4 | mcc | 1.0 | Documentation, Uses, and more | ||||
| gatk | lcc, mcc | 1.0 | GATK tools . | Variant Calling, Genotyping, Sequencing Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| gatk4 | lcc, mcc | 1.0 | GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discoverye. | Bioinformatics, Genomic Analysis, Variant Discovery, High-Throughput Sequencing | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| gaussian | lcc | N/A | Gaussian is a computational chemistry software for quantum mechanical simulations, widely used by researchers for studying molecular structures and reactions. It offers advanced capabilities in electronic structure prediction and various spectroscopic properties analysis. | Computational Chemistry, Quantum Chemistry, Molecular Modeling | Chemical Sciences, Natural Sciences | Simulation Software | Documentation, Uses, and more |
| gawk | ecc | N/A | GaussView aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output. Description Source: https://gaussian.com/gaussview6/ |
Text Processing, Data Manipulation, Pattern Scanning | Chemistry, Computer & Information Sciences | Text Processing Tool | Documentation, Uses, and more |
| gbs-snp-crop | lcc | 1.0 | Documentation, Uses, and more | ||||
| gcc | lcc, mcc | 1.0 | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). | Compiler, Software Development, Programming | Computer Science | Development Tools | Documentation, Uses, and more |
| gcc-c++ | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| gcc-gfortran | mcc | 1.0 | Documentation, Uses, and more | ||||
| gcc-runtime | ecc | N/A | The GCC Runtime Library is a part of the GCC compiler collection that provides runtime support for programs compiled with GCC. It includes various runtime libraries and support files necessary for programs compiled with GCC to execute correctly. | Compiler, Runtime, Library | Software Engineering, Systems & Development, Engineering & Technology | Runtime Library | Documentation, Uses, and more |
| gcc_linux-64 | lcc | 1.0 | Documentation, Uses, and more | ||||
| gcccore | lcc | N/A | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). | Compiler, Programming, Software Development | Computer & Information Sciences, Software Engineering, Systems & Development | Core Component | Documentation, Uses, and more |
| gdal | lcc | 1.0 | GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation. Description Source: https://gdal.org/ |
Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis | Earth & Environmental Sciences, Engineering & Technology | Library | Documentation, Uses, and more |
| gdbm | ecc | N/A | A library of database functions that use extensible hashing and works similar to the standard UNIX dbm functions. Description Source: https://github.com/conda-forge/gdbm-feedstock/blob/main/recipe/meta.yaml | Database Management, Key-Value Store, Persistent Storage, Api | Computer & Information Sciences | Library | Documentation, Uses, and more |
| geant4 | lcc, mcc | 1.0 | Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. | Software, Physics, Simulation, Particle Transport | Particle Physics, Physical Sciences | Toolkit | Documentation, Uses, and more |
| genomescope2 | mcc | 1.0 | Genomescope2: Reference-free profiling of polyploid genomes | Genome Analysis, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| genometools | mcc | 1.0 | Documentation, Uses, and more | ||||
| getorganelle | lcc | 1.0 | Getorganelle is a fast and versatile toolkit for accurate de novo assembly of organelle genomes. | Bioinformatics, Genomics, Molecular Biology, Computational Biology | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| gettext | ecc, lcc | N/A | GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation | Internationalization, Localization, Software Development | Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| gfacpp | mcc | 1.0 | Documentation, Uses, and more | ||||
| gff3tool | lcc | 1.0 | Documentation, Uses, and more | ||||
| gff3toolkit | lcc | 1.0 | Documentation, Uses, and more | ||||
| ggplot2 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| ghostscript | lcc | 1.0 | Ghostscript is an interpreter for the PostScript® language and PDF files. It is available under either the GNU GPL Affero license or licensed for commercial use from Artifex Software, Inc. Ghostscript consists of a PostScript interpreter layer and a graphics library. Description Source: https://ghostscript.com/ |
Document-Processing, File-Conversion, Print-Management | Computer & Information Sciences, Engineering & Technology | Software Development | Documentation, Uses, and more |
| gist-pipeline | lcc | 1.0 | Documentation, Uses, and more | ||||
| gistpipeline | lcc | 1.0 | Documentation, Uses, and more | ||||
| git | lcc, mcc | 1.0 | Git is a distributed version control system, widely used for tracking changes in source code during software development. It allows multiple developers to work collaboratively on a project, providing tools for managing versions, resolving conflicts, and maintaining a history of changes made to the codebase. | Version Control, Software Development, Source Code Management | Computer & Information Sciences, Software Engineering, Systems & Development | Development Tools | Documentation, Uses, and more |
| git-lfs | lcc | N/A | git-lfs software. | Version Control, File Storage, Git Extension | Engineering & Technology | Development Tool | Documentation, Uses, and more |
| gizmo | lcc | N/A | Documentation, Uses, and more | ||||
| gklib | mcc | 1.0 | A library of various helper routines and frameworks used by Karypis Lab software such as METIS. | Geometric Kernels, Computational Geometry, Algorithms | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| glib | ecc | N/A | GLib is a general-purpose, portable utility library, which provides many useful data types, macros, type conversions, string utilities, file utilities, a mainloop abstraction, and so on. It is one of the base libraries of GTK+. Description Source: https://docs.gtk.org/glib/ |
Utility Library, C Programming, Data Structures, Memory Management, Thread Support | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| glib2-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| glibc | ecc | N/A | glibc, the GNU C Library, is an essential part of most systems running the Linux kernel. It provides the necessary functionality for programs written in the C programming language to interact with the operating system and hardware. | C Library, Operating System, System Programming | Computer & Information Sciences | Library | Documentation, Uses, and more |
| glibc-langpack-en | mcc | 1.0 | Documentation, Uses, and more | ||||
| glibc-static | mcc | 1.0 | Documentation, Uses, and more | ||||
| glimpse | mcc | 1.0 | Documentation, Uses, and more | ||||
| glimpse-bio | mcc | 1.0 | Documentation, Uses, and more | ||||
| glnexus | lcc, mcc | 1.0 | Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects. | Variant Calling, Genotyping, Haplotype-Aware, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| glnexus-1.4.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| globus-cli | lcc | N/A | A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. | Command-Line Interface, File Transfer Service, Data Management, Data Transfer | Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| gmake | ecc | N/A | Documentation, Uses, and more | ||||
| gmap | lcc | 1.0 | Gmap is a genomic mapping and alignment program for mRNA and EST sequences. | Bioinformatics, Computational Biology, Genomics, Transcriptomics, RNA-Seq | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gmes_linux_64 | lcc | 1.0 | Documentation, Uses, and more | ||||
| gmp | ecc | N/A | GNU MP is a portable library written in C for arbitrary precision arithmetic on integers, rational numbers, and floating-point numbers. It aims to provide the fastest possible arithmetic for all applications that need higher precision than is directly supported by the basic C types. Description Source: https://gmplib.org/manual/Introduction-to-GMP |
Computational Software, Library, Mathematics, Software Development | Pure Mathematics, Mathematics | Library | Documentation, Uses, and more |
| gmsh | lcc, mcc | 1.0 | Mesh software . | mesh generation, finite element analysis, CAD, post-processing | Engineering, Finite Element Analysis | Mesh Generator | Documentation, Uses, and more |
| gnu | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu-parallel | mcc | 1.0 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel. Description Source: https://www.gnu.org/software/parallel/ |
Documentation, Uses, and more | |||
| gnu12 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu14 | ecc, lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu7 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnu8 | lcc | N/A | GNU Compiler Family (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| gnupg | lcc | 1.0 | Documentation, Uses, and more | ||||
| go | ecc | N/A | Go is expressive, concise, clean, and efficient. Its concurrency mechanisms make it easy to write programs that get the most out of multicore and networked machines, while its novel type system enables flexible and modular program construction. Go compiles quickly to machine code yet has the convenience of garbage collection and the power of run-time reflection. It's a fast, statically typed, compiled language that feels like a dynamically typed, interpreted language. Description Source: https://go.dev/doc/ |
Documentation, Uses, and more | |||
| go-bootstrap | ecc | N/A | go-bootstrap is a Go programming language template project that provides a starting point for building Go applications with a predefined project structure, configuration, and best practices. | Go, Template, Project Structure, Best Practices | Engineering & Technology | Template Project | Documentation, Uses, and more |
| go-md2man | ecc | N/A | Documentation, Uses, and more | ||||
| gocryptfs | ecc | N/A | Documentation, Uses, and more | ||||
| gompi | lcc | N/A | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. | Hpc, Parallel Computing, Mpi, Distributed Computing | Engineering & Technology | Documentation, Uses, and more | |
| gperf | ecc | N/A | GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. Description Source: https://www.gnu.org/software/gperf/ |
Perfect Hash Function, Hash Table, Optimization, Gnu | Computer Science, Computer & Information Sciences | Compiler/Generator | Documentation, Uses, and more |
| graphaligner | mcc | 1.0 | Documentation, Uses, and more | ||||
| graphviz | lcc | N/A | Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. | Graph Visualization, Diagramming, Open Source Software | Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| grep | ecc | N/A | Documentation, Uses, and more | ||||
| grid | lcc | 1.0 | Documentation, Uses, and more | ||||
| gridss | lcc | 1.0 | Gridss is a module software suite containing tools useful for the detection of genomic rearrangements. | Structural Variant Calling, DNA Sequencing, Genomic Rearrangements | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| groff | mcc | 1.0 | groff (GNU roff) is a typesetting system that reads plain text input files that include formatting commands to produce output in PostScript, PDF, HTML, or DVI formats or for display to a terminal. Formatting commands can be low-level typesetting primitives, macros from a supplied package, or user-defined macros. All three approaches can be combined. Description Source: https://www.gnu.org/software/groff/ |
Typesetting, Text Formatting, Unix Utilities | Computer & Information Sciences | Typesetting System | Documentation, Uses, and more |
| gromacs | lcc | N/A | GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. | Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems | Chemistry, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| gromacs-plumed2 | lcc | N/A | Documentation, Uses, and more | ||||
| gromacs-plumed2-gpu | lcc | N/A | Documentation, Uses, and more | ||||
| gsalign | mcc | 1.0 | Documentation, Uses, and more | ||||
| gsl | lcc, mcc | 1.0 | GNU Scientific Library (GSL) | Numerical Library, Mathematical Functions, C Programming, C++ Programming | Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| gsl-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| gtdbtk | mcc | 1.0 | GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. | Documentation, Uses, and more | |||
| gtf2csv | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| gth-1.7.3-linux_x86_64 | lcc | 1.0 | Documentation, Uses, and more | ||||
| gtools | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| gubbins | lcc | 1.0 | Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. | Bacterial Recombination, Whole-Genome Sequencing, Population Genetics | Bioinformatics, Biological Sciences | Documentation, Uses, and more | |
| guidance | lcc | 1.0 | Documentation, Uses, and more | ||||
| guppy | mcc | 1.0 | Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' production basecalling algorithms and several bioinformatic post-processing features. It is run from the command line in Windows, Mac OS, and on multiple Linux platforms. Guppy is also integrated with our sequencing instrument software, MinKNOW, and a subset of Guppy features are available via the MinKNOW UI. A selection of configuration files allows basecalling of DNA and RNA libraries made with Oxford Nanopore Technologies’ current sequencing kits, in a range of flow cells. Description Source: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview |
Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing | Genomics, Biological Sciences | Basecaller | Documentation, Uses, and more |
| h5py | lcc | 1.0 | The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want. Description Source: https://www.h5py.org/ |
Python Library, Data Storage, Numerical Data, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| hdf5 | lcc | N/A | HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. | File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing | Other Computer & Information Sciences | Library/Tool | Documentation, Uses, and more |
| help2man | lcc | N/A | help2man produces simple manual pages from the '--help' and '--version' output of other commands. | Documentation, Man Pages, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| herro | lcc | 1.0 | Documentation, Uses, and more | ||||
| hic-pro | lcc | N/A | Hic-Pro | Bioinformatics, Genomics, Chromatin Structure, Hi-C Data, Data Visualization, Chromatin Interactions | Genomics, Biological Sciences | Data Analysis | Documentation, Uses, and more |
| hicpro | mcc | 1.0 | Documentation, Uses, and more | ||||
| hicup | lcc | N/A | Documentation, Uses, and more | ||||
| hifiasm | mcc | 1.0 | Hifiasm is fast haplotype-resolved de novo assembler for PacBio HiFi reads. | Assembler, De Novo Assembly | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| hifiasm-0.25.0 | mcc | 1.0 | Documentation, Uses, and more | ||||
| hisat | lcc | 1.0 | Documentation, Uses, and more | ||||
| hisat2 | lcc, mcc | 1.0 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs (Sirén et al. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first implementation. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). Description Source: https://daehwankimlab.github.io/hisat2/ |
Alignment, Ngs, Genomics, Transcriptomics | Biology, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| hmmer | lcc, mcc | 1.0 | HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Description Source: http://hmmer.org/ |
Bioinformatics, Computational Biology, Proteomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| hmmer2go | lcc | 1.0 | Documentation, Uses, and more | ||||
| hocort | mcc | 1.0 | Documentation, Uses, and more | ||||
| homer | lcc, mcc | 1.0 | HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. Description Source: http://homer.ucsd.edu/homer/motif/ |
Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| htseq | lcc | 1.0 | HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. | Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| htslib | lcc, mcc | 1.0 | HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. Description Source: https://github.com/samtools/htslib |
Bioinformatics, Sequencing Data, File Format Processing, C Library | Genomics, Biological Sciences | Data Processing | Documentation, Uses, and more |
| humann | lcc, mcc | 1.0 | Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). | Metagenomics, Microbiome, Pathway Analysis, Bioinformatics | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| humann2 | lcc | 1.0 | Documentation, Uses, and more | ||||
| hwloc | lcc | N/A | The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. | Machine Topology, Hardware Architecture, System Software | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hyphy | lcc | 1.0 | Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. | Bioinformatics, Molecular Evolution, Phylogenetics, Epidemiology | Bioinformatics, Biological Sciences | Open-Source Software | Documentation, Uses, and more |
| hyphy-analysis | lcc | N/A | Documentation, Uses, and more | ||||
| hypo | mcc | 1.0 | HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. | Statistical Analysis, Hypothesis Testing, Data Analysis | Statistics & Probability | Scientific Software | Documentation, Uses, and more |
| hypre | lcc | N/A | Scalable algorithms for solving linear systems of equations | Preconditioners, Solvers, Linear Systems, Sparse Matrices | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| icc | lcc | N/A | Intel C and C++ compilers | Documentation, Uses, and more | |||
| icc32 | lcc | N/A | Documentation, Uses, and more | ||||
| iccifort | lcc | N/A | Intel C, C++ & Fortran compilers | Compiler, High-Performance Computing, Optimization | Engineering & Technology | Programming Tool | Documentation, Uses, and more |
| idr | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| ifort | lcc | N/A | Intel Fortran compiler | Documentation, Uses, and more | |||
| ifort32 | lcc | N/A | Intel® Fortran Compiler Classic for building optimized Intel® 64, and IA-32 CPUs | Documentation, Uses, and more | |||
| iimpi | lcc | N/A | Intel C/C++ and Fortran compilers, alongside Intel MPI. | Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis | Bioinformatics, Biological Sciences | Analytical Tool | Documentation, Uses, and more |
| imagemagick | lcc, mcc | 1.0 | ImageMagick https://imagemagick.org/script/install-source.php | Image Processing, Graphics Editing, Conversion Tool | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| imagemagick-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| imagemagick-libs | mcc | 1.0 | Documentation, Uses, and more | ||||
| imb | lcc | N/A | Intel MPI Benchmarks (IMB) | Benchmarking, In-Memory Databases | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| imkl | lcc | N/A | Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. | Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Open-Source | Documentation, Uses, and more |
| impi | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Message Passing Library, Parallel Computing, Asynchronous Messaging | Engineering & Technology | Communication Library | Documentation, Uses, and more |
| impi/2018.3.222 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| impi/2019.3.199 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| impi/2019.4.243 | lcc | N/A | Intel MPI Library (C/C++/Fortran for x86_64) | Documentation, Uses, and more | |||
| implicit-landuse | lcc | 1.0 | Documentation, Uses, and more | ||||
| init_opencl | lcc | N/A | init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications. | Software, Compiler, Library, Hpc | Computer & Information Sciences | Software Development | Documentation, Uses, and more |
| inotify-tools | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| inspector | lcc, mcc | 1.0 | Inspector is a software tool used for monitoring and analyzing various aspects of computer systems and networks to detect and prevent security breaches or performance issues. | Monitoring, Security, Network Analysis | Computer Science, Computer & Information Sciences | Security Software | Documentation, Uses, and more |
| intel | lcc | N/A | Intel Compiler Family (C/C++/Fortran for x86_64) | Semiconductor, Technology, Microprocessors | Engineering & Technology | Hardware | Documentation, Uses, and more |
| intel-oneapi-compilers | lcc | N/A | Documentation, Uses, and more | ||||
| intel-oneapi-mpi | lcc | N/A | Documentation, Uses, and more | ||||
| intel_ipp_ia32 | lcc | N/A | Documentation, Uses, and more | ||||
| intel_ipp_intel64 | ecc, lcc | N/A | A library of multimedia and data processing optimized for Single Instruction, Multiple Data (SIMD) instructions. | Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography | Computer & Information Sciences, Software Engineering, Systems & Development | Commercial | Documentation, Uses, and more |
| intel_ippcp_ia32 | lcc | N/A | Intel Integrated Performance Primitives - Cryptography (IPP-Crypto) is a library that provides highly optimized building blocks for a variety of encryption and decryption algorithms on Intel architecture processors. It aims to accelerate cryptographic operations to enhance performance in software applications. | Cryptographic Library, Performance Optimization, Intel Architecture | Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| intel_ippcp_intel64 | ecc, lcc | N/A | Intel Integrated Performance Primitives Cryptography (IPP Cryptography) is a collection of highly optimized cryptographic functions and algorithms developed by Intel for high-performance computing applications. It provides a set of cryptographic functions optimized for Intel processors to enhance the security and performance of cryptographic operations in software. | Cryptography, High-Performance Computing, Intel Processors, Security | Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| intelpython3_full | lcc | N/A | Documentation, Uses, and more | ||||
| interproscan | lcc, mcc | 1.0 | Interproscan is the software package that allows sequences to be scanned against InterPro's member database signatures. | Bioinformatics, Proteomics, Sequence Analysis, Functional Annotation | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| interproscan-5.73-104.0 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| iphop | mcc | 1.0 | Documentation, Uses, and more | ||||
| ipykernel | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| ipyparallel | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| ipyrad | lcc | N/A | Documentation, Uses, and more | ||||
| ipython | lcc, mcc | 1.0 | IPython is BSD-licensed, open-source software that is developed as a set of Subprojects under the ipython Github organization. These Subprojects are all part of the larger Project Jupyter umbrella. For further information about project governance, sponsorship and development, please see the Project page on Jupyter’s website. Description Source: https://ipython.org/project.html |
Command Shell, Interactive Computing, Data Visualization, Parallel Computing, Data Analysis | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| iqtree | mcc | 1.0 | IQ-TREE is an efficient phylogenomic software by maximum likelihood. | Documentation, Uses, and more | |||
| iqtree-2.2.0_beta | mcc | 1.0 | Documentation, Uses, and more | ||||
| isoseq | mcc | 1.0 | Documentation, Uses, and more | ||||
| isoseq3 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| itac | lcc | N/A | The Intel® Trace Analyzer and Collector profiles and analyzes MPI applications to help focus your optimization efforts. Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/trace-analyzer.html#gs.4oj2fp |
Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jags | lcc | 1.0 | JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. Description Source: https://mcmc-jags.sourceforge.io/ |
Bayesian Statistics, Hierarchical Modeling, Mcmc Simulation | Statistics & Probability, Mathematics | Statistical Modeling | Documentation, Uses, and more |
| jasper | lcc | N/A | The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. | Image Processing, Open-Source, Jpeg-2000 | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| java | lcc, mcc | 1.0 | Java jdk-11.0.2 | Programming Language, Computing Platform | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| java-jdk | mcc | 1.0 | Documentation, Uses, and more | ||||
| jellyfish | lcc, mcc | 1.0 | Jellyfish is a fast and memory-efficient software for counting k-mers in DNA sequences, which are commonly used in genome analysis and sequence assembly. It provides algorithms for k-mer counting, storage, and querying to extract valuable insights from biological data. | K-Mer Counting, DNA Sequences, Sequence Analysis | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| jmodeltest | lcc | N/A | jmodeltest. | Documentation, Uses, and more | |||
| joblib | lcc | 1.0 | Documentation, Uses, and more | ||||
| juicebox_env | mcc | 1.0 | Documentation, Uses, and more | ||||
| julia | lcc | N/A | Julia 1.1.0 | Programming Language, Technical Computing, High-Performance Computing, Scientific Computing, Numerical Analysis | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jupyter | mcc | 1.0 | JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning. | Data Science, Scientific Computing, Machine Learning | Computer & Information Sciences | Web Application | Documentation, Uses, and more |
| jupyter_contrib_nbextensions | mcc | 1.0 | Documentation, Uses, and more | ||||
| jupyterlab | ecc, lcc, mcc | 1.0 | JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning. | Interactive Computing, Data Visualization, Jupyter Notebooks, Web-Based Interface, Code Editing | Computer & Information Sciences | Data Science Tool | Documentation, Uses, and more |
| kaiju | mcc | 1.0 | Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database. | Bioinformatics, Computational Biology, Genomics, Sequencing Data | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| kallisto | lcc, mcc | 1.0 | Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. | RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kat | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| keras | ecc | 1.0 | Keras is a deep learning API written in Python and capable of running on top of either JAX, TensorFlow, or PyTorch. Description Source: https://keras.io/about/ |
Neural Networks, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| kernel-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| kmc | mcc | 1.0 | Kmc is a tool for efficient k-mer counting and filtering of reads based on k-mer content. | Sequence Analysis, Genome Assembly, Metagenomics | Computational Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| kneaddata | lcc, mcc | 1.0 | Kneaddata is a tool designed to perform quality control on metagenomic sequencing data. | Bioinformatics, Metagenomics, Data Quality Control | Biomolecular Sciences, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| kount | lcc | 1.0 | Documentation, Uses, and more | ||||
| kraken-biom | lcc | 1.0 | Documentation, Uses, and more | ||||
| kraken2 | mcc | 1.0 | Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Description Source: https://github.com/DerrickWood/kraken2/wiki/About-Kraken-3 |
Documentation, Uses, and more | |||
| kraken2-2.1.3 | mcc | 1.0 | Documentation, Uses, and more | ||||
| krakenuniq | mcc | 1.0 | Documentation, Uses, and more | ||||
| lammps | lcc | N/A | Large-scale Atomic/Molecular Massively Parallel Simulator | Molecular Dynamics, Simulation, Computational Chemistry | Physical Chemistry, Chemical Sciences | Code/Package | Documentation, Uses, and more |
| lammpss-deepmd-kit-module-cpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| lammpss-deepmd-kit-module-gpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| lapack-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| laser | mcc | 1.0 | Documentation, Uses, and more | ||||
| lastz | lcc | 1.0 | LASTZ - pairwise DNA sequence aligner | Bioinformatics, DNA Sequencing, Alignment, Comparative Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| latex | lcc | N/A | LaTeX is a typesetting system commonly used for scientific and technical documentation preparation. It is widely used for the communication and publication of scientific documents in fields such as mathematics, computer science, physics, engineering, and more. | Typesetting, Scientific Communication, Document Preparation | Natural Sciences, Mathematics, Computer & Information Sciences, Engineering & Technology | Publishing | Documentation, Uses, and more |
| lcc-user | lcc | N/A | Documentation, Uses, and more | ||||
| lcc-users | lcc | N/A | Documentation, Uses, and more | ||||
| ldheatmap | lcc | 1.0 | Documentation, Uses, and more | ||||
| lefse | mcc | 1.0 | Documentation, Uses, and more | ||||
| less | mcc | 1.0 | Documentation, Uses, and more | ||||
| lftp | mcc | 1.0 | lftp is a file transfer program that allows sophisticated FTP, HTTP and other connections to other hosts. If site is specified then lftp will connect to that site otherwise a connection has to be established with the open command. | File Transfer | Command Line Tool | Documentation, Uses, and more | |
| lhapdf | lcc | 1.0 | Documentation, Uses, and more | ||||
| libarchive-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| libbamtools-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libboost-all-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libboost-iostreams-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libbsd | ecc | N/A | libbsd is a library that provides a collection of functions from the FreeBSD operating system for enhancing compatibility and portability across different Unix-like systems. It includes various system-related functions that are widely used in Unix programming to access system services and perform low-level operations. | Library, Bsd, Operating System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libbz2-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libcairo2-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libcrypto++-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libcurl | mcc | 1.0 | Documentation, Uses, and more | ||||
| libcurl-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| libcurl4-gnutls-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libcurl4-openssl-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libeigen3-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libexpat1-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libfabric | ecc | N/A | Development files for the libfabric library | Fabric Interfaces, High-Performance Computing, Communication Resources | Computer Science, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| libffi | ecc | N/A | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. FFI stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface. Description Source: https://github.com/libffi/libffi |
Library, Portability, Calling Conventions | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libffi-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libfontconfig1-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libfreetype6-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libfribidi-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libfuse | ecc | N/A | Documentation, Uses, and more | ||||
| libgl1-mesa-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libglvnd-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| libgpg-error | ecc | N/A | libgpg is a library that provides an API for interacting with GnuPG (GNU Privacy Guard) for encryption, decryption, and key management tasks. It allows developers to integrate GnuPG functionality into their applications. | Error Handling, Library, Gnupg | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libgsl-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libharfbuzz-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libhts-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libiconv | ecc | N/A | libiconv provides an iconv() implementation, for use on systems which don't have one, or whose implementation cannot convert from/to Unicode. Description Source: https://www.gnu.org/software/libiconv/#TOCintroduction |
Character Set Conversion, Text Data, Encoding | Other Computer & Information Sciences, Computer & Information Sciences | Conversion Tool | Documentation, Uses, and more |
| libjpeg-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| liblpsolve55-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| liblzma-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libmd | ecc | N/A | libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials. | Molecular Dynamics, Simulation, Library | Physical Sciences | Computational | Documentation, Uses, and more |
| libmysql++-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libncurses-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libncurses5-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libncursesw5-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libnsl | mcc | 1.0 | Public client interface library for NIS(YP) Description Source: https://github.com/conda-forge/libnsl-feedstock/blob/main/recipe/meta.yaml | Network Services, Communication, Protocols | Computer & Information Sciences | System Software | Documentation, Uses, and more |
| libnvidia-gl | lcc | 1.0 | Documentation, Uses, and more | ||||
| libopencv-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libpciaccess | lcc | N/A | Generic PCI access library. | Library, Pci Bus Access, User-Space Drivers | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libpng-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libpng-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| libpython3-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libreadline | lcc | N/A | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | Command-Line Interface, Text Editing, Gnu Library, Interactive Programs | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libseccomp | ecc | N/A | libseccomp is a library for implementing secure computing mode (seccomp) filters in Linux systems. It enables developers to apply fine-grained filtering on system calls, restricting the actions that processes can perform for improved system security. | Syscall Filtering, Linux Kernel, Security | Computer & Information Sciences | Development | Documentation, Uses, and more |
| libsigsegv | ecc | N/A | libsigsegv is a library for handling segmentation fault signals in Unix-like systems. It provides a mechanism for detecting, handling, and recovering from segment violation errors during program execution. | Library, Memory, Page Fault | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libsqlite3-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libssl-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libstdc++-static | mcc | 1.0 | Documentation, Uses, and more | ||||
| libsuitesparse-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| libtiff5-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| libtool | ecc, lcc | 1.0 | autoamke software. | Library Management, Software Development, Compilation | Engineering & Technology | Utility/Tool | Documentation, Uses, and more |
| libv8-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libxcrypt | ecc | N/A | Documentation, Uses, and more | ||||
| libxml2 | ecc, lcc | N/A | Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). | Xml, Html, Parsing, Validation, Manipulation | Computer & Information Sciences | Parsing | Documentation, Uses, and more |
| libxml2-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| libxslt1-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| liftoff | mcc | 1.0 | Liftoff is an accurate GFF3/GTF lift over pipeline. | Build System, Ios Development, Macos Development, Software Development, Apple Platforms | Engineering & Technology | Build Automation | Documentation, Uses, and more |
| ligpargen | lcc | N/A | Documentation, Uses, and more | ||||
| likwid | lcc | N/A | Toolsuite of command line applications for performance oriented programmers | Performance Analysis, Hpc, Performance Counter Profiling, Hardware Performance Counters | Performance Evaluation & Benchmarking, Engineering & Technology | Tool | Documentation, Uses, and more |
| lima | lcc, mcc | 1.0 | Lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. | Single-Cell RNA-Seq, Data Analysis, Transcriptomics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| llama | ecc | 1.0 | Documentation, Uses, and more | ||||
| llvm5 | lcc | N/A | LLVM Compiler Infrastructure | Documentation, Uses, and more | |||
| lmod | ecc, lcc, mcc | N/A | Lmod: An Environment Module System | Module Management, Software Environment, Environment Module System | Infrastructure & Instrumentation, Engineering & Technology | Utility | Documentation, Uses, and more |
| locale-gen | mcc | 1.0 | Documentation, Uses, and more | ||||
| locales | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| longshot | mcc | 1.0 | Documentation, Uses, and more | ||||
| longstitch | mcc | 1.0 | Documentation, Uses, and more | ||||
| ltr_retriever | mcc | 1.0 | Documentation, Uses, and more | ||||
| lua | ecc | N/A | Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. | Programming Language, Scripting Language, Embedded Systems | Computer & Information Sciences | Documentation, Uses, and more | |
| lua-luafilesystem | ecc | N/A | Documentation, Uses, and more | ||||
| lua-luaposix | ecc | N/A | Documentation, Uses, and more | ||||
| lumerical | lcc | N/A | Lumerical software. | Documentation, Uses, and more | |||
| lz4 | ecc | N/A | LZ4 is lossless compression algorithm, providing compression speed > 500 MB/s per core (>0.15 Bytes/cycle). It features an extremely fast decoder, with speed in multiple GB/s per core (~1 Byte/cycle). A high compression derivative, called LZ4_HC, is available, trading customizable CPU time for compression ratio. Description Source: https://lz4.org/ |
Compression, Data Compression, Lossless Compression | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| lzma-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| lzo | ecc | N/A | LZO offers pretty fast compression and extremely fast decompression. MiniLZO is a very lightweight subset of the LZO library. Description Source: https://github.com/conda-forge/lzo-feedstock/blob/main/recipe/meta.yaml | Data Compression, Algorithm, High-Speed | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| m4 | ecc, lcc | N/A | GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. | Macro Processor, Text Processing, Software Development, Build Process | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| maaslin2 | lcc | 1.0 | Documentation, Uses, and more | ||||
| macs | lcc | 1.0 | Documentation, Uses, and more | ||||
| macs2 | lcc, mcc | 1.0 | MACS2 is Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites. | Chip-Seq Analysis, Transcription Factor Binding Sites, Histone Modification, Bioinformatics | Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| mafft | lcc, mcc | 1.0 | MAFFT is a multiple alignment program for amino acid or nucleotide sequences. | Bioinformatics, Sequence Alignment, Phylogenetics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| make | lcc, mcc | 1.0 | Make is an open-source, tool designed to build, test and package software. | Build Automation, Software Development, Programming | Engineering & Technology | Utility | Documentation, Uses, and more |
| maker | lcc, mcc | 1.0 | Maker is a portable and easily configurable genome annotation pipeline. | Genome Annotation, Bioinformatics | Genomics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| mamba | mcc | 1.0 | Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. | Package Manager, Dependency Resolver, Environment Management | Engineering & Technology | Package Manager | Documentation, Uses, and more |
| maple | lcc | N/A | maple tool designed to package software. | Documentation, Uses, and more | |||
| mapsplice | lcc | N/A | Documentation, Uses, and more | ||||
| marty | lcc | 1.0 | Documentation, Uses, and more | ||||
| mash-linux64 | mcc | 1.0 | Documentation, Uses, and more | ||||
| mashmap | lcc, mcc | 1.0 | Mashmap is a fast approximate aligner for long DNA sequences. | Mapping, Alignment, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| mashtree | lcc | 1.0 | Mashtree is a tool to create a tree using Mash distances. | Phylogenetic Trees, Genomic Similarity, Mash Distances | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| masurca | lcc, mcc | 1.0 | The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner. | Genome Assembly, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| matlab | lcc | N/A | MATLAB | Programming Language, Technical Computing, Visualization, Mathematical Notation | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| matplotlib | ecc, lcc, mcc | 1.0 | Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible. Description Source: https://matplotlib.org/ |
Python Library, Data Visualization, Plotting Library | Computer & Information Sciences | Plotting & Graphing Tool | Documentation, Uses, and more |
| mcclintock | ecc, mcc | 1.0 | Documentation, Uses, and more | ||||
| mcl | lcc | 1.0 | Mcl is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs | Clustering, Network Analysis, Graph Algorithms | Computer & Information Sciences | Clustering Algorithm | Documentation, Uses, and more |
| mcscanx | mcc | 1.0 | MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. | Gene Synteny, Genomic Analysis, Syntenic Relationships | Biological Sciences | Tool | Documentation, Uses, and more |
| mdanalysis | lcc | 1.0 | Documentation, Uses, and more | ||||
| mdtraj | lcc | 1.0 | Documentation, Uses, and more | ||||
| medaka | mcc | 1.0 | Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. | Bioinformatics, Ngs Data Analysis, Nanopore Sequencing, Consensus Sequence Calling | Biological Sciences | Ngs Data Analysis Tool | Documentation, Uses, and more |
| megahit | lcc, mcc | 1.0 | Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. | Metagenome Assembly, Bioinformatics, Sequencing Data, Snp-Aware, Draft Assemblies | Bioinformatics, Biological Sciences | Assembly Software | Documentation, Uses, and more |
| megahit-1.2.9 | mcc | 1.0 | Documentation, Uses, and more | ||||
| megan | lcc | 1.0 | Megan is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample. | Metagenomics, Microbiome, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| megax | lcc | 1.0 | Documentation, Uses, and more | ||||
| meryl | lcc | N/A | Meryl is a genomic k-mer counter (and sequence utility) with nice features. | Bioinformatics, Genomics, K-Mer Counting | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mesa-libgl | lcc | 1.0 | Documentation, Uses, and more | ||||
| meshio | lcc | N/A | Documentation, Uses, and more | ||||
| meshlab | mcc | 1.0 | Documentation, Uses, and more | ||||
| meson | ecc | N/A | Meson is an open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible. Description Source: https://mesonbuild.com/ |
Build System, Software Development, Automation | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| metabat2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| metaphlan | lcc, mcc | 1.0 | Metaphlan is computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. | Metagenomics, Microbiome, Microbial Ecology, Bioinformatics | Environmental Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| methods | lcc | 1.0 | Documentation, Uses, and more | ||||
| methpipe | mcc | 1.0 | Documentation, Uses, and more | ||||
| methyldackel | lcc, mcc | 1.0 | Methyldackel is a (mostly) universal methylation extractor for BS-seq experiments. | DNA Methylation, Bisulfite Sequencing, Epigenetics | Genetics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| metis | lcc | N/A | Metis development files | Computational Software, Graph Partitioning, Mesh Partitioning, Hypergraph Partitioning | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mfem | lcc | N/A | Lightweight, general, scalable C++ library for finite element methods | Finite Element Method, C++ Library, Parallel Computing | Engineering & Technology | Library | Documentation, Uses, and more |
| microbecensus | mcc | 1.0 | Documentation, Uses, and more | ||||
| microbecensus-sourceapp | mcc | 1.0 | Documentation, Uses, and more | ||||
| migrate-n | lcc | N/A | Documentation, Uses, and more | ||||
| miniconda3 | lcc | N/A | Miniconda is a free minimal installer for conda. It is a small bootstrap version of Anaconda that includes only conda, Python, the packages they both depend on, and a small number of other useful packages (like pip, zlib, and a few others). If you need more packages, use the conda install command to install from thousands of packages available by default in Anaconda’s public repo, or from other channels, like conda-forge or bioconda. Description Source: https://docs.anaconda.com/free/miniconda/index.html |
Package Management, Dependency Management, Software Installation | Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| miniforge3 | lcc | N/A | Documentation, Uses, and more | ||||
| minigraph | lcc | 1.0 | Documentation, Uses, and more | ||||
| minimap | mcc | 1.0 | Documentation, Uses, and more | ||||
| minimap2 | lcc, mcc | 1.0 | minimap2 software. | Sequence Alignment, Bioinformatics, Genomics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| miranda | mcc | 1.0 | Documentation, Uses, and more | ||||
| mirdeep | lcc | 1.0 | Documentation, Uses, and more | ||||
| mirdeep2 | lcc, mcc | 1.0 | miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...). | Bioinformatics, Computational Biology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| mitobim | lcc | 1.0 | Documentation, Uses, and more | ||||
| mitofinder | lcc | 1.0 | Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data. | Bioinformatics, Genomics, Mitochondrial Genomes, Next-Generation Sequencing, Annotation | Genomics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| mitohifi | lcc | 1.0 | Documentation, Uses, and more | ||||
| mitoz | lcc | 1.0 | Documentation, Uses, and more | ||||
| mkl | ecc, lcc | N/A | Intel Compiler Family (C/C++/Fortran for x86_64) | Mathematical Library, Optimized Computations, Thread-Safe Functions | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| mkl32 | lcc | N/A | The Intel® oneAPI Math Kernel Library (oneMKL) helps you achieve maximum performance with a math computing library of highly optimized, extensively parallelized routines for CPU and GPU. The library has C and Fortran interfaces for most routines on CPU, and SYCL interfaces for some routines on both CPU and GPU. Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html#gs.4ofwv10 |
Mathematics, Computational Software, Hpc Tools | Other Mathematics | Library | Documentation, Uses, and more |
| mmseqs2 | lcc | 1.0 | Mmseqs2 is a software suite to search and cluster huge protein and nucleotide sequence sets. | Sequence Searching, Sequence Clustering, Bioinformatics, Computational Biology | Biological Sciences | Sequence Search & Clustering Tool | Documentation, Uses, and more |
| molpro | lcc | N/A | Molpro software. | Documentation, Uses, and more | |||
| momap | lcc | N/A | momap software. | Documentation, Uses, and more | |||
| mono | lcc | N/A | mono software. | Documentation, Uses, and more | |||
| moose | lcc | 1.0 | MOOSE (Multiphysics Object-Oriented Simulation Environment) is a finite element simulation framework designed for solving complex multiphysics and multiscale engineering problems. It provides a flexible and extensible platform for researchers and engineers to develop and deploy simulation tools for a wide range of applications. | Simulation, Multiphysics, Finite Element Method | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| mosdepth | mcc | 1.0 | Documentation, Uses, and more | ||||
| mothur | lcc, mcc | 1.0 | Mothur is an open source software package for bioinformatics data processing. | Bioinformatics, Microbial Communities, High-Throughput Sequencing | Microbial Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| mpdaf | lcc | 1.0 | Documentation, Uses, and more | ||||
| mpdaf-3.5-fitsio | lcc | 1.0 | Documentation, Uses, and more | ||||
| mpfr | ecc | N/A | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPFR has continuously been supported by the INRIA and the current main authors come from the Caramba and AriC project-teams at Loria (Nancy, France) and LIP (Lyon, France) respectively; see more on the credit page. MPFR is based on the GMP multiple-precision library. Description Source: https://www.mpfr.org/ |
Arbitrary-Precision Arithmetic, Floating-Point Computation, Mathematical Library | Mathematics | Computational Software | Documentation, Uses, and more |
| mpi | ecc, lcc | N/A | Intel(R) MPI Library | Hpc, Parallel Computing, Message Passing, Scalable Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpi4py | lcc, mcc | 1.0 | Mpi4py provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI specification and exposes an API which grounds on the standard MPI-2 C++ bindings. Description Source: https://pypi.org/project/mpi4py/ |
Parallel Computing, Message Passing Interface, Python Library | Computer & Information Sciences, Other Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| mpich | ecc, lcc | N/A | MPICH MPI implementation | Mpi Implementation, Parallel Computing, High Performance Computing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpip | lcc | N/A | mpiP: a lightweight profiling library for MPI applications. | Software Utility, Hpc, Mpi Libraries, Cluster Management, Installation Tool | Engineering & Technology | Documentation, Uses, and more | |
| mrbayes | lcc, mcc | 1.0 | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. | Bayesian Inference, Phylogenetics, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Software Tool | Documentation, Uses, and more |
| multiqc | lcc, mcc | 1.0 | Multiqc is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools. | Bioinformatics, Computational Biology, Data Analysis, Reporting Tool | Biophysics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| mumax3 | lcc | 1.0 | Documentation, Uses, and more | ||||
| mummer4 | lcc | 1.0 | Mummer4 is a versatile alignment tool for DNA and protein sequences. | Bioinformatics, Sequence Alignment, Genomics | Genomics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| mumps | lcc | N/A | A MUltifrontal Massively Parallel Sparse direct Solver | Linear Algebra, Sparse Matrices, Computational Science, Engineering | Applied Mathematics, Mathematics | Solver | Documentation, Uses, and more |
| muscle | lcc, mcc | 1.0 | Muscle is a modified progressive alignment algorithm which has comparable accuracy to MAFFT, but faster performance. | Sequence Alignment, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mvapich2 | lcc | N/A | OSU MVAPICH2 MPI implementation | Mpi Implementation, High Performance Computing, Infiniband, Open-Source | Physical Sciences | Library/Tool | Documentation, Uses, and more |
| namd | lcc | N/A | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Molecular Dynamics, Biomolecular Systems, Parallel Computing, Cuda, Simulation | Biophysics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| nanocomp | mcc | 1.0 | Documentation, Uses, and more | ||||
| nanofilt | mcc | 1.0 | Nanofilt is a tool for filtering and trimming of Oxford Nanopore Sequencing data. | Bioinformatics, Sequence Analysis, Nanopore Sequencing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| nanoplot | mcc | 1.0 | Nanoplot is a plotting tool for long read sequencing data and alignments. | Bioinformatics, Genomics, Sequencing Data, Quality Control, Visualization | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ncbi-blast+ | lcc | 1.0 | Documentation, Uses, and more | ||||
| ncl | lcc | 1.0 | NCL is an interpreted language designed specifically for scientific data analysis and visualization. | Scientific Data Analysis, Data Visualization, Atmospheric Sciences | Environmental Sciences, Earth & Environmental Sciences | Scripting Language | Documentation, Uses, and more |
| ncurses | ecc, lcc | N/A | The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. | Programming Library, Text-Based User Interfaces, Terminal Applications | Computer Science, Computer & Information Sciences | Programming/Development | Documentation, Uses, and more |
| ncview | lcc | 1.0 | Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher. Description Source: https://cirrus.ucsd.edu/ncview/ |
Data Visualization, Netcdf, Earth System Data | Earth & Environmental Sciences | Data Analysis Tool | Documentation, Uses, and more |
| netcdf | lcc | N/A | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Scientific Data, Data Storage, Data Access, Data Formats, Data Manipulation, Data Visualization | Other Natural Sciences | Library | Documentation, Uses, and more |
| netcdf-cxx | lcc | N/A | C++ Libraries for the Unidata network Common Data Form | Netcdf, C++ | Earth & Environmental Sciences | Data Processing | Documentation, Uses, and more |
| netcdf-fortran | lcc | N/A | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Scientific Data, Fortran Interface, Netcdf Library | Other Natural Sciences | Programming Interface | Documentation, Uses, and more |
| netcdf-intel | lcc | N/A | Documentation, Uses, and more | ||||
| netifaces | mcc | 1.0 | Documentation, Uses, and more | ||||
| networkx | lcc, mcc | 1.0 | NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Description Source: https://networkx.org/ |
Python Library, Graph Theory, Network Analysis, Data Visualization | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| nextflow | lcc | 1.0 | Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Description Source: https://www.nextflow.io/ |
Workflow Manager, Computational Biology, Data Science | Biological Sciences | Open Source | Documentation, Uses, and more |
| ngenomesyn | mcc | 1.0 | Documentation, Uses, and more | ||||
| nghttp2 | ecc | N/A | This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API. | Http/2, Web Protocol, Networking | Computer & Information Sciences | Library | Documentation, Uses, and more |
| nginx | lcc | 1.0 | Documentation, Uses, and more | ||||
| ngsdist | lcc | 1.0 | ngsDist is a program for estimating pairwise genetic distances while explicitly accounting for uncertainty in genotype assignment. Instead of relying on traditional genotype calling, it operates directly on genotype likelihoods or posterior probabilities. | Documentation, Uses, and more | |||
| ngsld | mcc | 1.0 | ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. | Ngs, Bioinformatics, Genomics, Sequencing | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ngstools | lcc | 1.0 | Documentation, Uses, and more | ||||
| ngsutils | lcc | 1.0 | Ngsutils is suite of software tools for working with next-generation sequencing datasets. | Ngs, Bioinformatics, Sequencing, Data Analysis | Biological Sciences | Research Tools | Documentation, Uses, and more |
| ninja | ecc, mcc | 1.0 | Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible. Description Source: https://github.com/ninja-build/ninja |
Build System, Software Development, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| nltk | ecc | 1.0 | Natural Language Toolkit Description Source: https://github.com/conda-forge/nltk-feedstock/blob/main/recipe/meta.yaml | Python Library, Text Processing, Natural Language Processing | Informatics, Analytics & Information Science, Computer & Information Sciences | Text Analysis | Documentation, Uses, and more |
| nonpareil | mcc | 1.0 | Documentation, Uses, and more | ||||
| notebook | ecc, lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| notung | lcc | N/A | Documentation, Uses, and more | ||||
| novoplasty | lcc | 1.0 | Documentation, Uses, and more | ||||
| nri-md | lcc | 1.0 | Documentation, Uses, and more | ||||
| ntlink | mcc | 1.0 | Documentation, Uses, and more | ||||
| numactl | lcc | N/A | The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. | Numa, Memory Management, Performance Optimization | Other Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| numba | lcc, mcc | 1.0 | Numba is an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code. Description Source: https://numba.pydata.org/ |
Jit Compiler, Python Optimization, Numpy Optimization | Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| numpy | ecc, lcc, mcc | 1.0 | NumPy is the fundamental package for scientific computing in Python. It is a Python library that provides a multidimensional array object, various derived objects (such as masked arrays and matrices), and an assortment of routines for fast operations on arrays, including mathematical, logical, shape manipulation, sorting, selecting, I/O, discrete Fourier transforms, basic linear algebra, basic statistical operations, random simulation and much more. Description Source: https://numpy.org/doc/stable/user/whatisnumpy.html |
Scientific Computing, Numerical Computing, Data Analysis, Mathematics | Computer & Information Sciences, Mathematics | Computational Software | Documentation, Uses, and more |
| nvhpc | lcc | N/A | The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. Description Source: https://developer.nvidia.com/hpc-sdk |
Hpc, Gpu Acceleration, Compilers, Libraries, Development Tools | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| nvidia-rapids | lcc | 1.0 | The RAPIDS data science framework is a collection of libraries for running end-to-end data science pipelines completely on the GPU. The interaction is designed to have a familiar look and feel to working in Python, but utilizes optimized NVIDIA CUDA primitives and high-bandwidth GPU memory under the hood. | GPU Computing,Data Science,Machine Learning,Open Source | Data Analytics | Library | Documentation, Uses, and more |
| nwchem | lcc | N/A | NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of forcefields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations. Description Source: https://raw.githubusercontent.com/wiki/nwchemgit/nwchem/Capabilities.md |
Computational Chemistry, High-Performance Computing, Open-Source Software | Physical Chemistry, Chemical Sciences | Computational Chemistry Software | Documentation, Uses, and more |
| ocelot | lcc | N/A | Documentation, Uses, and more | ||||
| ocelot_api | lcc | N/A | Documentation, Uses, and more | ||||
| ocl-icd-opencl-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| oclfpga | lcc | N/A | The Intel® oneAPI DPC++/C++ Compiler provides optimizations that help your applications run faster on Intel® 64 architectures on Windows* and Linux*, with support for the latest C, C++, and SYCL language standards. This compiler produces optimized code that can run significantly faster by taking advantage of the ever-increasing core count and vector register width in Intel® Xeon® processors and compatible processors. Description Source: https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/get-started-guide/2024-0/overview.html |
Opencl, Fpga, Acceleration | Engineering & Technology | Framework | Documentation, Uses, and more |
| ocr | lcc | N/A | Open Community Runtime (OCR) for shared memory | Documentation, Uses, and more | |||
| ohpc | ecc, lcc | N/A | OpenHPC is a collaborative, community-driven effort to provide a comprehensive and cohesive open-source HPC stack to the community. Through close collaboration with key stakeholders across the industry, OpenHPC aims to provide a reference collection of open-source HPC software components and best practices to enable the development, testing, and deployment of HPC systems. Ultimately, building on the resecarch outputs from various related fields. | Hpc, High Performance Computing, Open-Source, Collaborative, Community-Driven | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| omb | lcc | N/A | OSU Micro-benchmarks | Documentation, Uses, and more | |||
| ont-guppy-cpu_3.0.3_linux64 | mcc | 1.0 | Documentation, Uses, and more | ||||
| openbabel | lcc, mcc | 1.0 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Description Source: https://openbabel.org/ |
Documentation, Uses, and more | |||
| openbabel311 | mcc | 1.0 | Documentation, Uses, and more | ||||
| openblas | lcc | N/A | OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. | Linear Algebra, Blas Library, Optimized Functions, Open Source | Mathematics, Computer & Information Sciences | Documentation, Uses, and more | |
| openblas-devel | lcc | 1.0 | Documentation, Uses, and more | ||||
| opencoarrays | lcc | N/A | ABI to leverage the parallel programming features of the Fortran 2018 DIS | Documentation, Uses, and more | |||
| opencv-python | ecc | 1.0 | Documentation, Uses, and more | ||||
| openjdk | ecc, lcc, mcc | 1.0 | OpenJDK is a free, Open-Source version of the Java Development Kit for the Java Platform, Standard Edition (Java SE). Description Source: https://openjdk.org/ |
Open-Source, Java Development, Software Development, Programming | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| openmm | lcc, mcc | 1.0 | OpenMM is a high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. We include extensive language bindings for Python, C, C++, and even Fortran. Description Source: https://openmm.org/ |
Molecular Dynamics, Biomolecular Simulations, Computational Chemistry, Biophysics, Gpu Acceleration | Bioinformatics, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| openmpi | lcc | 1.0 | The Open MPI Project is an open source MPI-3 implementation. | Mpi Library, Parallel Computing, High Performance Computing, Distributed Memory System | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| openmpi3 | lcc | N/A | A powerful implementation of MPI | Documentation, Uses, and more | |||
| openmpi4 | lcc | N/A | A powerful implementation of MPI | Library | Documentation, Uses, and more | ||
| openmpi5 | ecc | N/A | A powerful implementation of MPI/SHMEM | Documentation, Uses, and more | |||
| openpyxl | ecc | 1.0 | Documentation, Uses, and more | ||||
| opensees | lcc | N/A | OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. A number of OpenSees applications are released on this website. Description Source: https://opensees.berkeley.edu/ |
Simulation, Finite Element Analysis, Earthquake Engineering, Structural Analysis, Geotechnical Engineering | Civil Engineering, Engineering & Technology | Finite Element Analysis (Fea) | Documentation, Uses, and more |
| openssl | ecc | N/A | OpenSSL software is a robust, commercial-grade, full-featured toolkit for general-purpose cryptography and secure communication. Description Source: https://www.openssl.org/ |
Cryptography, Security, Encryption, Networking | Computer & Information Sciences, Other Computer & Information Sciences | Documentation, Uses, and more | |
| openssl-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| operams | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| optislang | lcc | N/A | Documentation, Uses, and more | ||||
| optparse | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| orca | lcc | N/A | ab initio molecular dynamics package | Quantum Chemistry, Computational Chemistry, Quantum Mechanics | Physical Chemistry, Chemical Sciences | Quantum Chemistry Software | Documentation, Uses, and more |
| orthofinder | lcc, mcc | 1.0 | Orthofinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. | Bioinformatics, Phylogenomics, Orthology, Gene Set Inference | Biological Sciences | Genome Analysis Software | Documentation, Uses, and more |
| os | ecc | N/A | Documentation, Uses, and more | ||||
| p4vasp | lcc | N/A | p4vasp | Documentation, Uses, and more | |||
| p7zip | ecc | N/A | p7zip is a port of 7za.exe for POSIX systems like Unix (Linux, Solaris, OpenBSD, FreeBSD, Cygwin, AIX, ...), MacOS X and also for BeOS and Amiga. Description Source: https://p7zip.sourceforge.net/ |
File Archiver, Compression Software, Command-Line Tool, Open-Source Software | Computer & Information Sciences | Documentation, Uses, and more | |
| paml | lcc | 1.0 | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It may be used to estimate parameters and test hypotheses to study the evolutionary process. Description Source: http://abacus.gene.ucl.ac.uk/software/paml.html |
Phylogenetics, Evolutionary Analysis, Maximum Likelihood, Phylogenetic Inference | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| pandas | ecc, lcc, mcc | 1.0 | Powerful data structures for data analysis, time series, and statistics Description Source: https://github.com/conda-forge/pandas-feedstock/blob/main/recipe/meta.yaml | Python Library, Data Manipulation, Data Analysis, Structured Data, Tabular Data | Informatics, Analytics & Information Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| papi | lcc | N/A | Performance Application Programming Interface | Performance Monitoring, Api, Hardware Counter | Engineering & Technology | Library | Documentation, Uses, and more |
| parallel | lcc, mcc | 1.0 | Parallel processing made simple and fast and runs any code in parallel processes(> use all CPUs), Threads(> speedup blocking operations), or Ractors(> use all CPUs). Description Source: https://github.com/grosser/parallel |
Parallel Computing, Command-Line Tool, Task Scheduling | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| parasail-python | mcc | 1.0 | Documentation, Uses, and more | ||||
| paraview | lcc, mcc | 1.0 | Paraview tools . | Visualization, Data Analysis, Open-Source, Multi-Platform | Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences | Data Visualization | Documentation, Uses, and more |
| partitionfinder | lcc | 1.0 | Documentation, Uses, and more | ||||
| patch | ecc, lcc | 1.0 | Documentation, Uses, and more | ||||
| patchelf | lcc | 1.0 | PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. | Dependency Management, Executable Modification, Dynamic Linker Paths | Computer & Information Sciences | Library Management | Documentation, Uses, and more |
| pathofact | lcc | N/A | Documentation, Uses, and more | ||||
| pb-assembly | lcc | 1.0 | Documentation, Uses, and more | ||||
| pbccs | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pbjelly | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pblat | mcc | 1.0 | pblat is parallelized blat with multi-threads support. | Bioinformatics, Sequence Alignment, Genomics, Parallel Computing | Genomics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| pbmm2 | lcc, mcc | 1.0 | Pbmm2 is a minimap2 frontend for PacBio native data formats. | Long Read Aligner, Graph-Guided Mapping, Reference Genome Mapping, Bioinformatics | Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| pbtk | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pcangsd | mcc | 1.0 | PCAngsd is a program that estimates the covariance matrix and individual allele frequencies for low-depth next-generation sequencing (NGS) data in structured/heterogeneous populations using principal component analysis (PCA) to perform multiple population genetic analyses using genotype likelihoods. | Population Genetics, Genomic Data Analysis | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| pcre | lcc | 1.0 | The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. NOTE:This version of PCRE is now at end of life, and is no longer being actively maintained. New Projects should use PCRE2 instead. Description Source: https://www.pcre.org/ |
Regular Expressions, Pattern Matching, Library | Biology, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| pcre2 | ecc | N/A | PCRE2 is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. NOTE: This is the current version of the PCRE library. Description Source: https://www.pcre.org/ |
Regular Expressions, Text Processing, Pattern Matching | Biology, Computer & Information Sciences | C Library | Documentation, Uses, and more |
| pdfminer.six | ecc | 1.0 | Documentation, Uses, and more | ||||
| pdftotext | lcc | N/A | Documentation, Uses, and more | ||||
| pdtoolkit | lcc | N/A | PDT is a framework for analyzing source code | Python Library, Exploratory Data Analysis, Data Preprocessing, Feature Selection, Visualization | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| perl | ecc, lcc, mcc | 1.0 | Larry Wall's Practical Extraction and Report Language | Programming Language, Text Processing, Scripting, Web Development, System Administration | Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| perl-app-cpanminus | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-bio-viennangs | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-bioperl | lcc, mcc | 1.0 | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. | Documentation, Uses, and more | |||
| perl-core | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-cpan | lcc | 1.0 | Documentation, Uses, and more | ||||
| perl-data-dumper | lcc | 1.0 | Documentation, Uses, and more | ||||
| perl-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-ipc-run | mcc | 1.0 | Documentation, Uses, and more | ||||
| perl-velvetoptimiser | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| petsc | lcc | N/A | Portable Extensible Toolkit for Scientific Computation | Scientific Computing, Computational Science, Numerical Analysis | Natural Sciences | Library | Documentation, Uses, and more |
| pggb | mcc | 1.0 | pggb builds pangenome variation graphs from a set of input sequences. | Performance Evaluation, Benchmarking, Computational Applications | Performance Evaluation & Benchmarking, Training | Documentation, Uses, and more | |
| pgi | lcc | N/A | The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. Description Source: https://developer.nvidia.com/hpc-sdk |
Hpc, Compilers, Parallel Programming | Engineering & Technology | Development Tool | Documentation, Uses, and more |
| pgi-cuda | lcc | N/A | Documentation, Uses, and more | ||||
| phangorn | lcc | 1.0 | Documentation, Uses, and more | ||||
| phasebook | mcc | 1.0 | Documentation, Uses, and more | ||||
| phaser | lcc | N/A | Documentation, Uses, and more | ||||
| phdf5 | lcc | N/A | A general purpose library and file format for storing scientific data | Parallel I/O, Phdf5, Hdf5, Large Datasets | Computer & Information Sciences | File Format | Documentation, Uses, and more |
| phylophlan | lcc | 1.0 | Documentation, Uses, and more | ||||
| phyluce | lcc | N/A | Documentation, Uses, and more | ||||
| phyml | lcc | 1.0 | PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. PhyML was designed to process moderate to large data sets and can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements. | phylogenetics,bioinformatics,maximum likelihood,tree estimation | Bioinformatics, Phylogenetics | Documentation, Uses, and more | |
| picard | lcc, mcc | 1.0 | Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification. Description Source: https://broadinstitute.github.io/picard/ |
Bioinformatics, Ngs, Hts, Sequencing Data, Sam, Bam, Vcf | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| picrust2 | mcc | 1.0 | Picrust2 is a software for predicting functional abundances based only on marker gene sequences. | Bioinformatics, Metagenomics, Microbiome Analysis, Functional Gene Prediction | Biological Sciences | Metagenomics Tool | Documentation, Uses, and more |
| pigz | ecc | N/A | pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. Description Source: https://zlib.net/pigz/ |
Compression, Parallel Processing, Utility, Command-Line Tool | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| pillow | ecc | 1.0 | Pillow is a Python Imaging Library (PIL) fork that provides extensive image processing capabilities in Python. It allows users to create, open, manipulate, and save various image file formats, making it a versatile tool for image editing, processing, and enhancement. | Image Processing, Python Library | Computer & Information Sciences, Software Engineering, Systems & Development | Library | Documentation, Uses, and more |
| pilon | lcc | 1.0 | Pilon is an automated genome assembly improvement and variant detection tool. | Genome Assembly, Genomics, Bioinformatics, Computational Biology | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| pip | ecc | 1.0 | Documentation, Uses, and more | ||||
| pipeline | mcc | 1.0 | Documentation, Uses, and more | ||||
| pkg-config | lcc | N/A | pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). | Compilation, Library Management, Build Process | Engineering & Technology | Utility | Documentation, Uses, and more |
| pkgconf | ecc | N/A | pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility. Description Source: http://pkgconf.org/ |
Package Configuration, Build Flags, Link Flags, System-Agnostic | Computer & Information Sciences | Package Configuration | Documentation, Uses, and more |
| pkgconfig | lcc | 1.0 | pkgconfig is a Python module to interface with the pkg-config command line tool for Python 3.3+. It can be used to find all pkg-config packages, check if a package exists, check if a package meets certain version requirements, return the version, among other functionality. Description Source: https://github.com/matze/pkgconfig/tree/master |
Compilation, Library Management, Software Development | Engineering & Technology | Tool | Documentation, Uses, and more |
| plascad | lcc | 1.0 | Documentation, Uses, and more | ||||
| plasma | lcc | N/A | Parallel Linear Algebra Software for Multicore Architectures | Documentation, Uses, and more | |||
| plink | lcc, mcc | 1.0 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Description Source: https://zzz.bwh.harvard.edu/plink/ |
Genetic Analysis, Genomic Data Analysis, Gwas, Genetic Epidemiology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| plink2 | mcc | 1.0 | Plink2 is a whole genome association analysis toolset. | Genomics, Association Analysis, Genotype-Phenotype Data | Biological Sciences | Tool | Documentation, Uses, and more |
| plot3d | lcc | 1.0 | Documentation, Uses, and more | ||||
| plotsr | mcc | 1.0 | Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies. | Plotting, Data Visualization, Python Library | Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| plumed | lcc | N/A | PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. Description Source: https://www.plumed.org/ |
Molecular Dynamics, Enhanced Sampling, Free Energy Calculations, Collective Variables | Chemistry, Biological Sciences | Library | Documentation, Uses, and more |
| plyr | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pmix | lcc | N/A | The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for inter-process communication. Two versions (PMI-1 and PMI-2) have been released as part of the MPICH effort, with PMI-2 demonstrating better scaling properties than its PMI-1 predecessor. Description Source: https://pmix.github.io/standard |
Process Management, Parallel Computing, High-Performance Computing, Data Exchange, Resource Management, Scalability | Engineering & Technology | Hpc Tool | Documentation, Uses, and more |
| pnetcdf | lcc | N/A | A Parallel NetCDF library (PnetCDF) | Parallel I/O, Netcdf Files, Scalability, Performance | Physical Sciences | I/O Library | Documentation, Uses, and more |
| popoolation | mcc | 1.0 | Documentation, Uses, and more | ||||
| prank | lcc | 1.0 | PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. | Sequence Alignment, Bioinformatics, Genomics, Phylogenetics | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| prank=v.150803 | lcc | 1.0 | Documentation, Uses, and more | ||||
| pretext-suite | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| prodigal | mcc | 1.0 | Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory. Description Source: https://www.psc.edu/resources/software/prodigal/ |
Gene Prediction, Microbial Genomes | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| prodigal-2.6.3 | mcc | 1.0 | Documentation, Uses, and more | ||||
| prokka | lcc | 1.0 | Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Description Source: https://github.com/tseemann/prokka |
Genome Annotation, Bioinformatics, Genomics | Genetics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| proovread | lcc | N/A | Documentation, Uses, and more | ||||
| prun | ecc, lcc | N/A | job launch utility for multiple MPI families | Parallel Computing, High-Performance Computing, Distributed Computing, Data Analysis, Computation | Other Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| psi4 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| psutil | mcc | 1.0 | Documentation, Uses, and more | ||||
| ptscotch | lcc | N/A | Graph, mesh and hypergraph partitioning library using MPI | Documentation, Uses, and more | |||
| pulp | mcc | 1.0 | Documentation, Uses, and more | ||||
| purge_dups | mcc | 1.0 | purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth. | Bioinformatics, Genomics, DNA Sequences | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| py-cython | ecc | N/A | Py-Cython is a compiler for writing C extensions for the Python language. It allows for combining Python and C code seamlessly to improve performance and efficiency. | Compiler, Python Library, Performance Optimization | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| py-pip | ecc | N/A | py-pip is the official installer for Python packages from the Python Package Index (PyPI). It is used to install and manage software packages written in Python. | Package Management, Python, Software Installation | Computer & Information Sciences, Software Engineering, Systems & Development | Package Management | Documentation, Uses, and more |
| py-setuptools | ecc | N/A | Setuptools is a package development process library designed to facilitate development and distribution of Python projects. It provides a common approach for managing project dependencies, packaging, and installation processes. | Python, Package Development, Distribution, Dependency Management | Computer Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| py-wheel | ecc | N/A | Documentation, Uses, and more | ||||
| py2-mpi4py | lcc | N/A | Python bindings for the Message Passing Interface (MPI) standard. | Documentation, Uses, and more | |||
| py2-numpy | lcc | N/A | NumPy array processing for numbers, strings, records and objects | Documentation, Uses, and more | |||
| py2-scipy | lcc | N/A | Scientific Tools for Python | Documentation, Uses, and more | |||
| py2.7-samtools | lcc | N/A | Documentation, Uses, and more | ||||
| py3-mpi4py | lcc | N/A | Python bindings for the Message Passing Interface (MPI) standard. | Documentation, Uses, and more | |||
| py3-numpy | lcc | N/A | NumPy array processing for numbers, strings, records and objects | Documentation, Uses, and more | |||
| py3-scipy | lcc | N/A | Scientific Tools for Python | Documentation, Uses, and more | |||
| pyamg | mcc | 1.0 | Documentation, Uses, and more | ||||
| pyani | mcc | 1.0 | Pyani is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity. | Bioinformatics, Computational Biology, Microbial Genomics | Biological Sciences | Genomics Tool | Documentation, Uses, and more |
| pyani-0.2.13.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| pybind11 | lcc | 1.0 | pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection. Description Source: https://github.com/pybind/pybind11 |
Software Development, Python Library, C++ Integration, Header-Only Library | Computer & Information Sciences | Interoperability | Documentation, Uses, and more |
| pydub | ecc | 1.0 | Documentation, Uses, and more | ||||
| pymatgen | mcc | 1.0 | Documentation, Uses, and more | ||||
| pymeshlab | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pymupdf | ecc | 1.0 | Documentation, Uses, and more | ||||
| pypy | lcc | N/A | PyPy is a fast, compliant alternative implementation of the Python programming language. It aims to provide a high-performance, flexible, and efficient interpreter for Python, while maintaining compatibility with the CPython reference implementation. | Python Interpreter, Alternative Implementation, Just-In-Time Compilation, High Performance | Computer & Information Sciences | Programming Language Implementation | Documentation, Uses, and more |
| pysam | lcc, mcc | 1.0 | Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. Description Source: https://github.com/pysam-developers/pysam |
Bioinformatics, Sequence Analysis, Sam/Bam Files, Python Module | Biological Sciences | Library | Documentation, Uses, and more |
| pytesseract | ecc | 1.0 | Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and “read” the text embedded in images. Python-tesseract is a wrapper for Google’s Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others. Description Source: https://pypi.org/project/pytesseract/ |
Ocr, Text Recognition, Image Processing | Computer & Information Sciences | Ocr Library | Documentation, Uses, and more |
| pytest | mcc | 1.0 | The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries. Description Source: https://docs.pytest.org/en/8.0.x/ |
Testing, Python, Framework | Computer & Information Sciences | Testing Framework | Documentation, Uses, and more |
| python | ecc, lcc, mcc | 1.0 | Python 3.10 installed via Conda environment. | Programming Language, Interpreted Language, High-Level Language | Computer & Information Sciences, Software Engineering, Systems & Development | Language | Documentation, Uses, and more |
| python-annoy | lcc | 1.0 | Documentation, Uses, and more | ||||
| python-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| python-devtools | mcc | 1.0 | Documentation, Uses, and more | ||||
| python-pip | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| python-venv | ecc | N/A | Documentation, Uses, and more | ||||
| python3 | mcc | 1.0 | Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. It supports multiple programming paradigms beyond object-oriented programming, such as procedural and functional programming. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++. It is also usable as an extension language for applications that need a programmable interface. Finally, Python is portable: it runs on many Unix variants including Linux and macOS, and on Windows. Description Source: https://docs.python.org/3/faq/general.html#what-is-python |
Programming Language, Scripting Language | Computer & Information Sciences, Computer Science, Other Computer & Information Sciences | Interpreter | Documentation, Uses, and more |
| python3-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| python3-matplotlib | lcc | 1.0 | Documentation, Uses, and more | ||||
| python3-pip | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| python3-pyqt5 | mcc | 1.0 | Documentation, Uses, and more | ||||
| python3-pyqt5.qtsvg | mcc | 1.0 | Documentation, Uses, and more | ||||
| python3-setuptools | mcc | 1.0 | Documentation, Uses, and more | ||||
| python3-venv | lcc | 1.0 | Documentation, Uses, and more | ||||
| python312_ml | mcc | 1.0 | Documentation, Uses, and more | ||||
| pytorch | lcc | 1.0 | PyTorch is an optimized tensor library for deep learning using GPUs and CPUs. Description Source: https://pytorch.org/docs/stable/index.html |
Machine Learning, Deep Learning, Numerical Computation, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| pytraj | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| pyvcf | mcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2 | lcc, mcc | 1.0 | QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. \r Description Source: https://qiime2.org/ |
Microbiome, Bioinformatics, Sequencing | Biology, Microbiology | Documentation, Uses, and more | |
| qiime2-amplicon | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2-shotgun | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2-tiny | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiime2amplicon | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiskit | lcc | 1.0 | Documentation, Uses, and more | ||||
| qiskit-aer-gpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| qtbase5-dev | mcc | 1.0 | Documentation, Uses, and more | ||||
| quantumespresso | lcc | N/A | Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Description Source: https://www.quantum-espresso.org/ |
Chemistry | Package | Documentation, Uses, and more | |
| quast | lcc | 1.0 | Quast is Quality Assessment Tool for Genome Assemblies. | Genome Assembly, Bioinformatics, Quality Assessment | Genomics, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| quorum | lcc | 1.0 | Documentation, Uses, and more | ||||
| r | lcc, mcc | 1.0 | R is a language and environment for statistical computing and graphics (S-Plus like). | Statistical Computing, Data Analysis, Statistical Graphics | Biostatistics, Medical & Health Sciences | Statistical Software | Documentation, Uses, and more |
| r-base | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-fastbaps | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-peer | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-plm | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-plm-1.6_5 | lcc | 1.0 | Documentation, Uses, and more | ||||
| r-satscan | lcc | N/A | Documentation, Uses, and more | ||||
| r-seurat | mcc | 1.0 | Documentation, Uses, and more | ||||
| r-wgcna | lcc | 1.0 | Documentation, Uses, and more | ||||
| racon | lcc, mcc | 1.0 | Racon is consensus module for raw de novo DNA assembly of long uncorrected reads. | Bioinformatics, Sequence Analysis, Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ragtag | lcc, mcc | 1.0 | Ragtag is a tool for fast reference-guided genome assembly scaffolding. | Assembly Improvement, Genome Alignment, Assembly Evaluation | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| raisd | mcc | 1.0 | Documentation, Uses, and more | ||||
| rapids | lcc | 1.0 | RAPIDS is a collection of open source software libraries and APIs that gives you the ability to execute end-to-end data science and analytics pipelines entirely on NVIDIA GPUs using familiar PyData APIs. Description Source: https://rapids.ai/learn-more/#about |
Data Science, Analytics, Gpu Computing | Computer & Information Sciences | Data Science | Documentation, Uses, and more |
| raxml | lcc, mcc | 1.0 | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Description Source: https://github.com/amkozlov/raxml-ng |
Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raxml-ng | lcc | 1.0 | Raxml-ng is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. | Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raxml-ng_v0.9.0 | lcc | N/A | Documentation, Uses, and more | ||||
| raxmlng | mcc | 1.0 | Documentation, Uses, and more | ||||
| rcorrector | mcc | 1.0 | Documentation, Uses, and more | ||||
| rdkit | mcc | 1.0 | RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. Description Source: https://github.com/rdkit/rdkit |
Cheminformatics, Molecular Modeling, Cheminformatics Toolkit | Chemical Sciences, Natural Sciences | Toolkit | Documentation, Uses, and more |
| re2c | ecc | N/A | re2c is a free and open-source lexer generator for C/C++, Go and Rust with a focus on generating fast code. It compiles regular expression specifications to deterministic finite automata and encodes them in the form of conditional jumps in the target language. This approach is generally faster than table-based lexers, and the generated code is easier to debug and understand. Description Source: https://re2c.org/ |
Lexer, Scanner, Regular Expressions, Dfa | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| readline | ecc, lcc | 1.0 | The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. | Gnu, Command Line Interface, Interactive Programs, Line Editing, History Manipulation | Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| readline-devel | lcc | 1.0 | The readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The default editing mode is Emacs, but this can be changed when the application is run. In Emacs mode, the command line can be edited using the standard Emacs keystrokes. | Software Development, Library, Command Line Editing | Engineering & Technology | Development | Documentation, Uses, and more |
| recon | mcc | 1.0 | Documentation, Uses, and more | ||||
| reditools1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| reditools2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| reindeer | lcc | 1.0 | Documentation, Uses, and more | ||||
| repeatafterme | mcc | 1.0 | Documentation, Uses, and more | ||||
| repeatmasker | lcc, mcc | 1.0 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | Genomics, Bioinformatics, Sequence Analysis, Repeat Detection | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| repeatmodeler | mcc | 1.0 | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. | Genomics, Bioinformatics, Repeat Sequences, De Novo Identification | Bioinformatics, Biological Sciences | Research Tool | Documentation, Uses, and more |
| repeatscout | mcc | 1.0 | RepeatScout is a tool to discover repetitive substrings in DNA. | Genomics, Bioinformatics, Computational Biology | Biological Sciences | Genomic Sequence Analysis | Documentation, Uses, and more |
| requests | ecc | 1.0 | Documentation, Uses, and more | ||||
| requirements.txt | mcc | 1.0 | Documentation, Uses, and more | ||||
| reshape2 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| revbayes | lcc | N/A | RevBayes -- Bayesian phylogenetic inference using probabilistic graphical models and an interactive language. | Phylogenetics, Bayesian Inference, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Probabilistic Programming Tool | Documentation, Uses, and more |
| reviewer | mcc | 1.0 | Documentation, Uses, and more | ||||
| rmblast | mcc | 1.0 | Documentation, Uses, and more | ||||
| rnabloom | mcc | 1.0 | Documentation, Uses, and more | ||||
| rnahybrid | mcc | 1.0 | Documentation, Uses, and more | ||||
| rnammer | lcc | 1.0 | Documentation, Uses, and more | ||||
| rnastructure | lcc | 1.0 | Documentation, Uses, and more | ||||
| roary | lcc | 1.0 | Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. | Bioinformatics, Genomics, Pan-Genome Analysis, Prokaryotic Genomes | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| root | lcc, mcc | 1.0 | ROOT is a framework for data processing, born at CERN, at the heart of the research on high-energy physics. Every day, thousands of physicists use ROOT applications to analyze their data or to perform simulations. Description Source: https://root.cern/about/ |
Data Analysis, Visualization, High-Energy Physics, Data Manipulation, Statistical Analysis | Particle & High-Energy Physics, Physical Sciences | Library | Documentation, Uses, and more |
| rosetta | lcc | N/A | rosetta software. | Documentation, Uses, and more | |||
| rsem | lcc, mcc | 1.0 | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. Description Source: https://github.com/deweylab/RSEM |
RNA-Seq, Transcriptomics, Gene Expression, Bioinformatics | Genomics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| rstan | lcc | N/A | R | Documentation, Uses, and more | |||
| rstudio | lcc | 1.0 | RStudio is an integrated development environment (IDE) for the R and Python. It includes a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management. Description Source: https://posit.co/products/open-source/rstudio/ |
Ide, Statistical Computing, Data Visualization, Programming | Other Natural Sciences | Ide | Documentation, Uses, and more |
| rsync | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| rvtests | mcc | 1.0 | Documentation, Uses, and more | ||||
| rweka | lcc | 1.0 | Documentation, Uses, and more | ||||
| sabre | lcc | 1.0 | Documentation, Uses, and more | ||||
| salmon | lcc, mcc | 1.0 | Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. | RNA-Seq, Transcript Expression Quantification | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| salome | lcc | N/A | salome software. | Documentation, Uses, and more | |||
| salsa2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| sambamba | mcc | 1.0 | Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. | Sam/Bam Files, High-Performance Tool, Parallel Processing, Genomics | Biological Sciences | Computational Software | Documentation, Uses, and more |
| samblaster | mcc | 1.0 | Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files. | Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| samtools | lcc, mcc | 1.0 | SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Description Source: https://samtools.sourceforge.net/ |
Sequence Analysis, Genomics, Bioinformatics | Bioinformatics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| samtools-bcftools-htslib | mcc | 1.0 | Documentation, Uses, and more | ||||
| sas | lcc | N/A | SAS | Documentation, Uses, and more | |||
| scalapack | lcc | N/A | The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. | Linear-Algebra, Numerical-Computing, Distributed-Computing, Parallel-Computing | Other, Physical Sciences | Library | Documentation, Uses, and more |
| scalasca | lcc | N/A | Toolset for performance analysis of large-scale parallel applications | Performance Analysis, Parallel Applications, Performance Optimization, Mpi Applications, Visualization | Software Engineering, Systems & Development, Computer & Information Sciences | Performance Analysis Tool | Documentation, Uses, and more |
| scflow | lcc | N/A | Documentation, Uses, and more | ||||
| scikit-learn | ecc | 1.0 | Scikit-learn is an open-source machine learning library for Python, known for its simplicity and accessibility. It provides a wide range of supervised and unsupervised learning algorithms, as well as tools for model fitting, data preprocessing, model selection, and evaluation. | Machine Learning, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Libraries | Documentation, Uses, and more |
| scipy | ecc, lcc, mcc | 1.0 | SciPy is a collection of mathematical algorithms and convenience functions built on NumPy . It adds significant power to Python by providing the user with high-level commands and classes for manipulating and visualizing data. Description Source: https://docs.scipy.org/doc/scipy-1.8.0/tutorial/general.html |
Scientific Computing, Numerical Algorithms, Python Library, Data Analysis, Signal Processing | Computer & Information Sciences, Other Computer & Information Sciences | Python | Documentation, Uses, and more |
| scons | lcc | 1.0 | SCons is an Open Source software construction tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software. Description Source: https://scons.org/ |
Build Tool, Software Construction, Automation, Python | Engineering & Technology | Build Tool | Documentation, Uses, and more |
| scorep | lcc | N/A | Scalable Performance Measurement Infrastructure for Parallel Codes | Documentation, Uses, and more | |||
| scotch | lcc | N/A | Graph, mesh and hypergraph partitioning library | Graph Partitioning, Mesh Partitioning, Parallel Computing, Distributed Memory | Software Engineering, Systems & Development, Computer & Information Sciences | Library | Documentation, Uses, and more |
| scte | mcc | 1.0 | Documentation, Uses, and more | ||||
| sda | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| seaborn | ecc | 1.0 | Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Description Source: https://github.com/conda-forge/seaborn-feedstock/blob/main/recipe/meta.yaml | Python Library, Data Visualization, Statistical Graphics | Computer & Information Sciences | Library | Documentation, Uses, and more |
| sed | ecc | N/A | Documentation, Uses, and more | ||||
| seqkit | mcc | 1.0 | Seqkit is a rapid tool for manipulating fasta and fastq files. | Sequence Manipulation, Fasta, Fastq | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| seqsero2 | lcc | 1.0 | Documentation, Uses, and more | ||||
| seqtk | mcc | 1.0 | Documentation, Uses, and more | ||||
| settarg | lcc, mcc | N/A | The settarg module works with Lmod to help developers manage their compiled software projects. It does so by making it easy to switch between optimized or debug builds; change compiler or other modules; and let the build system know about the changes. The secret of settarg is that it consolidates the state of a build into one environment variable called $TARG. Description Source: https://lmod.readthedocs.io/en/latest/310_settarg.html |
Compilers, Optimization, Performance Enhancement, Command-Line Tool | Computer & Information Sciences | Command-Line Utility | Documentation, Uses, and more |
| shapely | mcc | 1.0 | Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. | Python Library, Geospatial Analysis, Geometric Objects | Geographic Information Science, Earth & Environmental Sciences | Python Library | Documentation, Uses, and more |
| shasta | lcc | N/A | shasta software. | Genome Assembly, Long-Read Sequencing, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| shtools | lcc | N/A | Documentation, Uses, and more | ||||
| sibeliaz | mcc | 1.0 | Documentation, Uses, and more | ||||
| signalp | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| sigprofilerextractor | lcc | 1.0 | Documentation, Uses, and more | ||||
| singlem | mcc | 1.0 | SingleM is a tool for profiling shotgun metagenomes. | Microbial Genomics, Metagenomics, Genome Assembly, Variant Calling | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| singularity | lcc | N/A | Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments. Description Source: https://apptainer.org/ |
Containerization, Scientific Computing, Hpc, Research | Computer & Information Sciences, Engineering & Technology | Platform | Documentation, Uses, and more |
| singularity-devel | lcc | N/A | Documentation, Uses, and more | ||||
| sionlib | lcc | N/A | Scalable I/O Library for Parallel Access to Task-Local Files | I/O Interface, Scientific Data, Hdf5 Files | Documentation, Uses, and more | ||
| slepc | lcc | N/A | A library for solving large scale sparse eigenvalue problems | Eigenvalue Problems, Sparse Matrices, Parallel Computing | Other Mathematics | Numerical Computing | Documentation, Uses, and more |
| slow5tools | mcc | 1.0 | Documentation, Uses, and more | ||||
| snakemake | mcc | 1.0 | The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. Description Source: https://snakemake.readthedocs.io/en/stable/ |
Workflow Management, Reproducibility, Traceability, Bioinformatics, Computational Biology, Data Science | Other Computer & Information Sciences | Software | Documentation, Uses, and more |
| snap | lcc | 1.0 | Snap is a semi-HMM-based Nucleic Acid Parser -- gene prediction tool. | Network Analysis, Large Networks, Graph Algorithms | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| sniffles | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| sniffles-2.5.3 | lcc | 1.0 | Documentation, Uses, and more | ||||
| snippy | lcc | 1.0 | Snippy is a tool for rapid haploid variant calling and core genome alignment. | Haploid Variant Calling, Core Genome Alignments, Bacterial Isolates | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| snp-dists | lcc | 1.0 | Snp-dists is a tool to convert a FASTA alignment to SNP distance matrix. | Genomics, Bioinformatics, Sequence Analysis, Phylogenetics | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| snp-sites | lcc | 1.0 | Snp-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment. | Bioinformatics, Computational Biology, Genomics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| soapdenovo | lcc | 1.0 | Documentation, Uses, and more | ||||
| soapdenovo2 | lcc | 1.0 | Soapdenovo2 is a short-read assembly method to build de novo draft assembly. | De Novo Assembly, Short Reads, Illumina Platform | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| solote | mcc | 1.0 | Documentation, Uses, and more | ||||
| sortedcontainers | mcc | 1.0 | Documentation, Uses, and more | ||||
| sortmerna | lcc | N/A | SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering. | Bioinformatics, Hpc Tools, Computational Software | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spaceranger | lcc, mcc | 1.0 | Cell ranger tools . | Bioinformatics, Hpc Tools | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spack | ecc, lcc | N/A | Build and installation framework | Package Management, Software Installation, Dependency Management, Hpc, Scientific Computing | Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| spacy | ecc | 1.0 | spaCy is a free, open-source library for advanced Natural Language Processing (NLP) in Python. Description Source: https://spacy.io/usage/spacy-101#whats-spacy |
Nlp, Natural Language Processing, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| spades | lcc, mcc | 1.0 | SPAdes is a genome assembly software that is specifically designed for single-cell and multi-cell bacterial sequencing data. It uses a combination of de Bruijn graph algorithms and error correction methods to construct accurate genome sequences. | Genome Assembly, Bioinformatics, Computational Biology | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| splicev | lcc | N/A | Documentation, Uses, and more | ||||
| splishsplash | lcc | 1.0 | SPlisHSPlasH is an open-source library for the physically-based simulation of fluids and solids. The simulation in this library is based on the Smoothed Particle Hydrodynamics (SPH) method which is a popular meshless Lagrangian approach to simulate complex fluid effects. The SPH formalism allows an efficient computation of a certain quantity of a fluid particle by considering only a finite set of neighboring particles. One of the most important research topics in the field of SPH methods is the simulation of incompressible fluids. SPlisHSPlasH implements current state-of-the-art pressure solvers (WCSPH, PCISPH, PBF, IISPH, DFSPH, PF) to simulate incompressibility. Moreover, the library provides different methods to simulate viscosity, surface tension, vorticity, elasticity, and drag forces. | Documentation, Uses, and more | |||
| sqanti3 | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| sqlite | ecc | N/A | SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. Description Source: https://www.sqlite.org/ |
Relational Database, Sql, Database Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| squashfs | ecc | N/A | SquashFS is a compressed read-only filesystem with built-in compression providing space-efficient storage. It is commonly used in embedded systems, live CDs, and Linux distributions to compress filesystem images and reduce storage space requirements while maintaining efficient access to files. | Filesystem, Compression, Read-Only | Computer Science, Computer & Information Sciences | Filesystem | Documentation, Uses, and more |
| squashfuse | ecc | N/A | Documentation, Uses, and more | ||||
| squigualiser | mcc | 1.0 | Documentation, Uses, and more | ||||
| sra-tools | lcc, mcc | 1.0 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Description Source: https://github.com/ncbi/sra-tools |
Bioinformatics, Hpc Tools, Sequence Analysis, Data Processing, High-Throughput Sequencing | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| sratoolkit | lcc | N/A | sratoolkit software. | Biology | Documentation, Uses, and more | ||
| sshfs | ecc | N/A | Documentation, Uses, and more | ||||
| stacks | lcc, mcc | 1.0 | Stacks is a software pipeline for building loci from RAD-seq | Software, Computational Biology, Bioinformatics | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| star | lcc, mcc | 1.0 | STAR (Spliced Transcripts Alignment to a Reference) is a fast and highly accurate RNA sequencing read mapper. It aligns RNA-Seq reads to a reference genome or transcriptome, enabling comprehensive analysis of gene expression and alternative splicing. | Software, RNA-Seq, Read Aligner, Splice Junctions, Alternative Splicing | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| starfish | mcc | 1.0 | Documentation, Uses, and more | ||||
| stitch | mcc | 1.0 | Documentation, Uses, and more | ||||
| stringr | lcc | 1.0 | Documentation, Uses, and more | ||||
| stringtie | lcc, mcc | 1.0 | Stringtie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. | RNA-Seq, Transcript Assembly, Transcript Quantification | Biological Sciences | Transcriptomics Tool | Documentation, Uses, and more |
| structure | lcc, mcc | 1.0 | Structure is a software package for using multi-locus genotype data to investigate population structure. | Population Genetics, Population Structure, Genotype Analysis, Data Analysis | Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| structure_threader | mcc | 1.0 | Documentation, Uses, and more | ||||
| structures | lcc | N/A | Documentation, Uses, and more | ||||
| subread | lcc | N/A | Subread carries out high-performance read alignment, quantification and mutation discovery. It is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and DNA-seq reads. It uses a new mapping paradigm called seed-and-vote to achieve fast, accurate and scalable read mapping. Subread automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports INDEL detection and can map reads with both fixed and variable lengths. | Ngs, Bioinformatics, Sequencing, Alignment | Bioinformatics, Biological Sciences | Ngs Analysis | Documentation, Uses, and more |
| superlu | lcc | N/A | A general purpose library for the direct solution of linear equations | Linear Algebra, Sparse Matrix, Direct Solver, Computational Science | Applied Mathematics, Mathematics | Solver Library | Documentation, Uses, and more |
| superlu_dist | lcc | N/A | A general purpose library for the direct solution of linear equations | Linear Solver, Sparse Systems, Parallel Computing | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| svim-asm | lcc | 1.0 | Documentation, Uses, and more | ||||
| svn | mcc | 1.0 | Documentation, Uses, and more | ||||
| syny | mcc | 1.0 | Documentation, Uses, and more | ||||
| syri | mcc | 1.0 | Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements. | Network Analysis, Visualization, Complex Networks | Computer & Information Sciences | Network Analysis Tool | Documentation, Uses, and more |
| szip | lcc | N/A | Szip compression software, providing lossless compression of scientific data | Compression Tool, Scientific Data Sets, Hdf5 File Format | Other Natural Sciences, Engineering & Technology | Utility | Documentation, Uses, and more |
| tabix | mcc | 1.0 | Tabix is a tool and file format for indexing and querying large tab-delimited text files like genomic variants in Variant Call Format (VCF). It enables fast retrieval of genomic intervals and regions from indexed files, allowing efficient access to specific data entries without loading entire files into memory. | Genomic Data, Indexing, Querying | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| talon | mcc | 1.0 | Talon is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. | Long-Read RNA Sequencing, Transcript Isoform Analysis, Gene Expression Quantification | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| tama | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| tar | ecc | N/A | tar is a command-line utility used for archiving files and directories on Unix-based systems. It allows bundling multiple files and directories into a single archive file, often compressed using utilities like gzip or bzip2. tar is commonly used for backup, data transfer, and file compression tasks. | File Archiving, Compression, Terminal | Other, Computer & Information Sciences | File Management | Documentation, Uses, and more |
| tassel | lcc | 1.0 | canu software. | Bioinformatics, Genetic Analysis, Plant Biology | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| tau | lcc | N/A | Tuning and Analysis Utilities Profiling Package | Software, Compiler, Hpc Tools | Physical Sciences | Commercial | Documentation, Uses, and more |
| tbb | ecc, lcc | N/A | The Intel Threading Building Blocks (TBB) is a C++ library for parallel programming that enables developers to create multi-threaded applications efficiently. It offers high-level constructs for parallelism, task-based programming, and workload distribution, simplifying the development of scalable and performance-oriented applications. | Multicore Programming, Parallel Computing, C++ Library, High Performance Computing | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| tbb32 | lcc | N/A | Intel Threading Building Blocks (TBB) is a widely used C++ template library developed by Intel for parallel programming on multi-core processors. TBB provides higher-level abstractions for parallelism, making it easier to write code that can take advantage of multicore processors. | Parallel Programming, Multi-Core Processors, C++ Template Library, Intel | Computer & Information Sciences | Library | Documentation, Uses, and more |
| tcl | ecc | N/A | Tcl (Tool Command Language) is a powerful dynamic programming language suitable for a wide range of uses, including web and desktop applications, networking, administration, and testing. Description Source: https://www.tcl.tk/ |
Scripting Language, Dynamic Programming Language, Cross-Platform, Scripting | Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tcsh | lcc | N/A | Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. | Command-Line Interpreter, Shell Scripting, Unix-Like Operating Systems | Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| telseq | lcc | N/A | Documentation, Uses, and more | ||||
| tensorflow | ecc | 1.0 | TensorFlow is an open-source machine learning framework developed by the Google Brain team. It provides a comprehensive, flexible ecosystem of tools, libraries, and community resources that enables researchers and developers to build and deploy machine learning-powered applications easily. | Machine Learning, Deep Learning, Neural Networks, Model Training | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| tensorflow-gpu | lcc | 1.0 | Documentation, Uses, and more | ||||
| tetools | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| texinfo | ecc | N/A | Documentation, Uses, and more | ||||
| texlive-base | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-cm-super | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-collection-fontsrecommended | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-collection-latex | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-collection-latexrecommended | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-dvipng | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-latex | lcc | 1.0 | Documentation, Uses, and more | ||||
| texlive-type1cm | lcc | 1.0 | Documentation, Uses, and more | ||||
| tidyr | lcc | 1.0 | Documentation, Uses, and more | ||||
| tidytext | lcc | 1.0 | Documentation, Uses, and more | ||||
| time | lcc, mcc | 1.0 | The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. | Time, Measurement, Events, Synchronization | Other | Measurement & Timekeeping | Documentation, Uses, and more |
| tk | lcc, mcc | 1.0 | Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. | Gui, Python, Toolkit, Desktop Applications | Computer & Information Sciences, Computer Science, Software Engineering, Systems & Development | Library | Documentation, Uses, and more |
| tm | lcc | 1.0 | Documentation, Uses, and more | ||||
| tmhmm | lcc | 1.0 | Documentation, Uses, and more | ||||
| tokenizers | lcc | 1.0 | Documentation, Uses, and more | ||||
| tools | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| tophat | lcc | 1.0 | TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. | RNA-Seq, Splice Junction Mapper, Genomics | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| topicmodels | lcc | 1.0 | Documentation, Uses, and more | ||||
| torch | ecc | 1.0 | Documentation, Uses, and more | ||||
| torchaudio | ecc | 1.0 | Documentation, Uses, and more | ||||
| torchvision | ecc | 1.0 | torchvision is a PyTorch library that provides computer vision utilities and pre-trained models for deep learning-based image processing tasks. It offers various tools for data loading, transformation, and model architecture specifically designed for computer vision applications. | Deep Learning, Computer Vision, Image Processing | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning | Documentation, Uses, and more |
| totalview | lcc | N/A | TotalView is a scalable and interactive debugger for parallel and high-performance computing (HPC) applications. It provides advanced debugging features to help developers analyze and optimize the performance of parallel programs running on clusters or supercomputers. | Debugging, Performance Analysis, Hpc, Big Data, Machine Learning | Infrastructure & Instrumentation, Engineering & Technology | Development & Optimization Tools | Documentation, Uses, and more |
| tpmcalculator | lcc, mcc | 1.0 | TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. | Bioinformatics, Computational Biology, RNA-Seq, Transcriptomics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| tqdm | ecc, lcc | 1.0 | tqdm is a fast, extensible progress bar library for Python and command line applications. It provides a simple and customizable way to visualize the progress of iterative tasks, making it easier for users to track the execution of loops and tasks. | Progress Bar, Python, Data Visualization, Productivity Tool | Computer & Information Sciences | Package | Documentation, Uses, and more |
| trame | mcc | 1.0 | Documentation, Uses, and more | ||||
| transdecoder | lcc | 1.0 | Transdecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. | Bioinformatics, Computational Biology, Transcriptomics, Protein Prediction | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| transformers | ecc | 1.0 | State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch Description Source: https://github.com/conda-forge/transformers-feedstock/blob/main/recipe/meta.yaml | Nlp, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| transrate | lcc | 1.0 | Transrate is software for de-novo transcriptome assembly quality analysis. | Transcriptome Assembly, Quality Assessment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| transrate-tools | lcc | 1.0 | Documentation, Uses, and more | ||||
| travis | lcc | 1.0 | Documentation, Uses, and more | ||||
| travis-src | lcc | 1.0 | Documentation, Uses, and more | ||||
| trf | mcc | 1.0 | Documentation, Uses, and more | ||||
| trilinos | lcc | N/A | A collection of libraries of numerical algorithms | Scientific Computing, Numerical Analysis, Parallel Computing, Computational Physics | Biology, Engineering & Technology | Library | Documentation, Uses, and more |
| trim-galore | lcc, mcc | 1.0 | Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files. | Ngs Data Processing, Quality Control, Adapter Trimming | Biological Sciences | Data Processing Tool | Documentation, Uses, and more |
| trimmomatic | lcc, mcc | 1.0 | Trimmomatic is a widely-used tool in bioinformatics for the preprocessing and quality control of high-throughput sequencing data, such as those from next-generation sequencing platforms. It offers various functions to remove adapters, trim low-quality reads, and filter sequences based on user-defined parameters. | Ngs Data Processing, Quality Control, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| trinity | lcc, mcc | 1.0 | Trinity is a software tool used for de novo transcriptome assembly from RNA-Seq data. It is designed to reconstruct full-length transcripts and address the challenges of assembling transcriptomes without a reference genome, contributing to gene expression and functional analysis. | Bioinformatics, Computational Biology, Transcriptomics, RNA-Seq, De Novo Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trinityrnaseq | lcc | 1.0 | Documentation, Uses, and more | ||||
| trinotate | lcc | N/A | Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Bioinformatics, Computational Biology, Transcriptomics, Functional Annotation | Bioinformatics, Biological Sciences | Functional Annotation Tool | Documentation, Uses, and more |
| trnascan-se | lcc | 1.0 | tRNAscan-SE is a widely used software tool for the identification of transfer RNA (tRNA) genes in genomic sequences. It utilizes covariance models to predict tRNA structures and gene locations, providing valuable insights into tRNA biology and facilitating genomic annotation. | Bioinformatics, Genomics, Computational Biology, Sequence Analysis | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trtools | mcc | 1.0 | TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing. | Python Library, Data Transformation, Tabular Data, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| ucsc-bedgraphtobigwig | mcc | 1.0 | Documentation, Uses, and more | ||||
| ucsc-fatotwobit | lcc | N/A | Documentation, Uses, and more | ||||
| ucsc_utils | mcc | 1.0 | Documentation, Uses, and more | ||||
| ucx | ecc, lcc | N/A | UCX is a communication library implementing high-performance messaging | Communication Library, High-Performance Computing, Distributed Computing | Engineering & Technology | Communication Library | Documentation, Uses, and more |
| ukyaro427 | lcc | 1.0 | Documentation, Uses, and more | ||||
| ultra | mcc | 1.0 | Documentation, Uses, and more | ||||
| ultra-bioinformatics | mcc | 1.0 | Documentation, Uses, and more | ||||
| umf | ecc | N/A | Documentation, Uses, and more | ||||
| uncalled4 | mcc | 1.0 | Documentation, Uses, and more | ||||
| unzip | ecc, lcc, mcc | 1.0 | UnZip is a utility tool used for extracting and viewing files compressed in the ZIP format. It allows users to decompress ZIP archives, extract individual files, and preserve the directory structure of the compressed content. | File Extraction, Compression, Utility | Computer & Information Sciences | File Extraction | Documentation, Uses, and more |
| util-linux-uuid | ecc | N/A | util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique. | Uuid Generator, Command-Line Utility, Unique Identifier, Data Management | Computer Science, Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| valgrind | lcc | N/A | Memory debugging utilities | Debugging, Profiling, Development Tool | Computer & Information Sciences | Programming Tool | Documentation, Uses, and more |
| vamb | mcc | 1.0 | Documentation, Uses, and more | ||||
| variantbam | lcc | 1.0 | Documentation, Uses, and more | ||||
| vasp | lcc | N/A | The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Description Source: https://www.vasp.at/info/about/ |
Materials Modelling, Electronic Structure Calculations, Quantum-Mechanical Simulations, Dft Calculations, Molecular Dynamics | Chemistry, Physical Sciences, Engineering & Technology | Package | Documentation, Uses, and more |
| vcf2arlequindiploid | mcc | 1.0 | Documentation, Uses, and more | ||||
| vcflib | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| vcftools | lcc, mcc | 1.0 | VCFtools is a versatile set of tools for working with Variant Call Format (VCF) files commonly used in genetics and genomics research. It allows researchers to perform various operations on genetic variation data, such as filtering, summarizing, and analyzing genetic variants in VCF format. | Genetic Variation Analysis, Variant Call Format (Vcf), Population Genetics, Bioinformatics | Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| vcontact2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| velocyto | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| velocyto.py | mcc | 1.0 | Velocyto is a computational tool for the analysis of RNA velocity, which aims to estimate the future state of individual cells in single-cell RNA sequencing data. It provides algorithms for inferring the direction and rate of change in gene expression at the single-cell level, offering insights into cellular dynamics and differentiation. | Single-Cell RNA-Sequencing, RNA Velocity Analysis, Gene Expression Dynamics, Transcriptomic Analysis | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| velvet | lcc, mcc | 1.0 | Velvet is a sequence assembler for very short reads. | Genomics, Bioinformatics, Sequencing, Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| verifybamid2 | mcc | 1.0 | Documentation, Uses, and more | ||||
| verkko | mcc | 1.0 | Documentation, Uses, and more | ||||
| verkko-2.2.1 | mcc | 1.0 | Documentation, Uses, and more | ||||
| vg | mcc | 1.0 | Variation graphs (vg) provides tools for working with genome variation graphs. | Documentation, Uses, and more | |||
| vibrant | mcc | 1.0 | Documentation, Uses, and more | ||||
| viennarna | lcc | 1.0 | Viennarna is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. | RNA Secondary Structure, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Prediction & Analysis Tools | Documentation, Uses, and more |
| vim | lcc | 1.0 | Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often called a "programmer's editor," and so useful for programming that many consider it an entire IDE. It's not just for programmers, though. Vim is perfect for all kinds of text editing, from composing email to editing configuration files. | text editor,programming,open source,cross-platform | Software Development, Text Editing | Text Editor | Documentation, Uses, and more |
| vina | lcc, mcc | 1.0 | Autodock VINA software. | Documentation, Uses, and more | |||
| virsorter | mcc | 1.0 | Documentation, Uses, and more | ||||
| visit | lcc | N/A | Visit is an open-source, interactive parallel visualization and graphical analysis tool used for visualizing scientific data. It is particularly focused on large-scale simulations and post-processing of complex data sets, enabling researchers to analyze and present their data in a visually engaging manner. | Visualization, Data Analysis, Scientific Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Visualization Software | Documentation, Uses, and more |
| vmd | lcc | N/A | VMD https://www.ks.uiuc.edu/Research/vmd/ | Molecular Visualization, Molecular Dynamics, Structural Biology | Biophysics, Biochemistry & Molecular Biology, Biological Sciences | Molecular Visualization Tool | Documentation, Uses, and more |
| vpl | lcc | N/A | VPL (Virtual Programming Lab) is an online platform and learning environment for teaching and practicing programming concepts through interactive coding exercises and assignments. It provides a virtual environment where students can write, compile, and test code, allowing educators to create programming labs and assessments in various programming languages. | Visual Programming, Beginner-Friendly, Graphical Interface | Computer & Information Sciences | Language Programming | Documentation, Uses, and more |
| vtune | ecc, lcc | N/A | VTune Profiler, also known as Intel VTune, is a performance profiling tool developed by Intel. It enables developers to optimize software performance on Intel architecture platforms by providing detailed insights into application behavior, identifying performance bottlenecks, and suggesting optimizations. | Performance Optimization, Profiling, Intel Architecture | Computer & Information Sciences | Profiling Tool | Documentation, Uses, and more |
| wget | ecc, lcc, mcc | 1.0 | GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. | Download Manager, Command-Line Tool | Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| whatshap | lcc, mcc | 1.0 | Whatshap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. | Genomics, Bioinformatics, Variant Phasing | Biological Sciences | Tool | Documentation, Uses, and more |
| wheel | lcc | 1.0 | Documentation, Uses, and more | ||||
| which | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| winnowmap | mcc | 1.0 | Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. | Mapping, Alignment, Nanopore, Pacbio, Sequencing | Genetics, Biological Sciences | Sequence Alignment Tool | Documentation, Uses, and more |
| wrf | lcc | N/A | The Weather Research and Forecasting (WRF) Model represents a cutting-edge mesoscale system for numerical weather prediction, designed to serve both atmospheric research and practical forecasting needs. Description Source: https://www.mmm.ucar.edu/models/wrf |
Weather Forecasting, Numerical Modeling, Atmospheric Science | Earth & Environmental Sciences | Meteorological Modeling Software | Documentation, Uses, and more |
| wrf-python | lcc | 1.0 | A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model. | Meteorology, Data Analysis, Visualization, Python, Scientific Computing | Meteorology, Weather Forecasting | Library | Documentation, Uses, and more |
| xlrd | ecc | 1.0 | xlrd is a library for reading data and formatting information from Excel files in the historical .xls format | excel parsing, data extraction, spreadsheet processing | Computational Data Analysis, Computer Science | Library | Documentation, Uses, and more |
| xorg-dev | lcc | 1.0 | Documentation, Uses, and more | ||||
| xorg-macros | lcc | N/A | X.org macros utilities. | Build Tools, Autoconf Macros | Computer & Information Sciences | Library/Dependency | Documentation, Uses, and more |
| xvfb | mcc | 1.0 | Xvfb (X Virtual Frame Buffer) is a virtual X server that provides a virtual display framebuffer for running GUI applications without a physical display on Unix-like systems. It allows users to perform graphical operations in headless environments and is commonly used for automated testing and server-side applications. | Display Server, Headless, Virtual Display | Computer & Information Sciences | Virtual Display Server | Documentation, Uses, and more |
| xz | ecc, lcc | N/A | xz: XZ utilities | Compression, Data Compression, Open-Source | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| xz-devel | mcc | 1.0 | Documentation, Uses, and more | ||||
| yahs | mcc | 1.0 | YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. | Hi-C scaffolding, genome assembly, chromosome-scale assembly | Life Sciences, Bioinformatics | Documentation, Uses, and more | |
| yak | mcc | 1.0 | Documentation, Uses, and more | ||||
| ytorch | ecc | 1.0 | Documentation, Uses, and more | ||||
| zlib | lcc | N/A | zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. | Compression, Data Compression, File Compression, Deflate Algorithm | Computer & Information Sciences | Data Compression | Documentation, Uses, and more |
| zlib-devel | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| zlib-ng | ecc | N/A | Documentation, Uses, and more | ||||
| zlib1g | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| zlib1g-dev | lcc, mcc | 1.0 | Documentation, Uses, and more | ||||
| zstd | ecc, lcc | 1.0 | zstd (Zstandard) is a high-performance data compression library and command-line tool that offers fast compression and decompression speeds with the ability to achieve high compression ratios. It is designed to balance efficient compression and decompression with speed, making it suitable for various data processing and storage applications. | Compression, Data Compression, Algorithm | Computer Science, Computer & Information Sciences | Compression Algorithm | Documentation, Uses, and more |