Official git repository for Biopython (originally converted from CVS)
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data-science-at-the-command-lineby jeroenjanssens
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Data Science at the Command Line
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A simple and efficient tool to parallelize Pandas operations on all available CPUs
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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
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R toolkit for single cell genomics
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Repository for the main Dockerfile with the Openworm software stack and project-wide issues
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An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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RNA-seq aligner
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Single-cell analysis in Python. Scales to >1M cells.
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Conda recipes for the bioconda channel.
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A versatile pairwise aligner for genomic and spliced nucleotide sequences
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Official code repository for GATK versions 4 and up
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Tools (written in C using htslib) for manipulating next-generation sequencing data
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Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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gentle forced aligner
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Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
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Toolkit for processing sequences in FASTA/Q formats
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Data intensive science for everyone.
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single-cell-tutorialby theislab
Jupyter Notebook 1076 Version:Current
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License: No License (No License)Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
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A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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Aggregate results from bioinformatics analyses across many samples into a single report.
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MMseqs2: ultra fast and sensitive search and clustering suite
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Deep probabilistic analysis of single-cell omics data
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tools for working with genome variation graphs
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Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
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SRA Tools
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Cloud-native genomic dataframes and batch computing
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getting-started-with-genomics-tools-and-resourcesby crazyhottommy
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License: No License (No License)Unix, R and python tools for genomics and data science
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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bedtools - the swiss army knife for genome arithmetic
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Accelerated BLAST compatible local sequence aligner.
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:bar_chart: A universal enrichment tool for interpreting omics data
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A collection of links and notes on forced alignment tools
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Scripts to download genomes from the NCBI FTP servers
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RNAseq analysis notes from Ming Tang
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🧬 gget enables efficient querying of genomic reference databases
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Trinity RNA-Seq de novo transcriptome assembly
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Python and C++ code for reading and writing genomics data.
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A scalable pipeline for designing reconfigurable organisms
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A Java Virtual Machine and Bytecode-to-IL Converter for .NET
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C library for high-throughput sequencing data formats
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Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
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Bayesian haplotype-based genetic polymorphism discovery and genotyping.
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GUI/CommandLine Tool Box for biologistists to utilize NGS data.
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A high-performance, Pythonic language for bioinformatics
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Tools for mapping a sentence with arbitrary length to vector space
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:zap: :aquarius: Rapid prokaryotic genome annotation
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Deep probabilistic analysis of single-cell omics data
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Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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biopythonby biopython
Official git repository for Biopython (originally converted from CVS)
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data-science-at-the-command-lineby jeroenjanssens
Data Science at the Command Line
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pandarallelby nalepae
A simple and efficient tool to parallelize Pandas operations on all available CPUs
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deepvariantby google
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Python 2819Updated: 11 mo ago License: Permissive (BSD-3-Clause)
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seuratby satijalab
R toolkit for single cell genomics
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OpenWormby openworm
Repository for the main Dockerfile with the Openworm software stack and project-wide issues
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fastpby OpenGene
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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scanpyby scverse
Single-cell analysis in Python. Scales to >1M cells.
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bioconda-recipesby bioconda
Conda recipes for the bioconda channel.
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minimap2by lh3
A versatile pairwise aligner for genomic and spliced nucleotide sequences
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gatkby broadinstitute
Official code repository for GATK versions 4 and up
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samtoolsby samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
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bwaby lh3
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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rnaseq_tutorialby griffithlab
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
R 1248Updated: 11 mo ago License: Proprietary (Proprietary)
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seqtkby lh3
Toolkit for processing sequences in FASTA/Q formats
C 1154Updated: 11 mo ago License: Permissive (MIT)
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galaxyby galaxyproject
Data intensive science for everyone.
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single-cell-tutorialby theislab
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
Jupyter Notebook 1076Updated: 10 mo ago License: No License (No License)
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seqkitby shenwei356
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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MultiQCby ewels
Aggregate results from bioinformatics analyses across many samples into a single report.
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MMseqs2by soedinglab
MMseqs2: ultra fast and sensitive search and clustering suite
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scvi-toolsby scverse
Deep probabilistic analysis of single-cell omics data
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vgby vgteam
tools for working with genome variation graphs
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bcbio-nextgenby bcbio
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
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hailby hail-is
Cloud-native genomic dataframes and batch computing
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getting-started-with-genomics-tools-and-resourcesby crazyhottommy
Unix, R and python tools for genomics and data science
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picardby broadinstitute
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Java 873Updated: 10 mo ago License: Permissive (MIT)
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bedtools2by arq5x
bedtools - the swiss army knife for genome arithmetic
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diamondby bbuchfink
Accelerated BLAST compatible local sequence aligner.
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clusterProfilerby YuLab-SMU
:bar_chart: A universal enrichment tool for interpreting omics data
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forced-alignment-toolsby pettarin
A collection of links and notes on forced alignment tools
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ncbi-genome-downloadby kblin
Scripts to download genomes from the NCBI FTP servers
Python 759Updated: 11 mo ago License: Permissive (Apache-2.0)
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RNA-seq-analysisby crazyhottommy
RNAseq analysis notes from Ming Tang
Python 757Updated: 12 mo ago License: Permissive (MIT)
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ggetby pachterlab
🧬 gget enables efficient querying of genomic reference databases
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trinityrnaseqby trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
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nucleusby google
Python and C++ code for reading and writing genomics data.
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reconfigurable_organismsby skriegman
A scalable pipeline for designing reconfigurable organisms
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ikvmby ikvm-revived
A Java Virtual Machine and Bytecode-to-IL Converter for .NET
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htslibby samtools
C library for high-throughput sequencing data formats
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eteby etetoolkit
Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
Python 694Updated: 10 mo ago License: Strong Copyleft (GPL-3.0)
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freebayesby freebayes
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
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TBtoolsby CJ-Chen
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
Shell 683Updated: 1 y ago License: No License (No License)
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seqby seq-lang
A high-performance, Pythonic language for bioinformatics
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sentence2vecby klb3713
Tools for mapping a sentence with arbitrary length to vector space
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prokkaby tseemann
:zap: :aquarius: Rapid prokaryotic genome annotation
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scvi-toolsby YosefLab
Deep probabilistic analysis of single-cell omics data
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pysamby pysam-developers
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
C 658Updated: 11 mo ago License: Permissive (MIT)
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khmerby dib-lab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
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