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    fidelram/deepTools

    Tools to process and analyze deep sequencing data.

    python bioinformatics rna-seq genomics ngs chip-seq

    Updated Jul 14, 2017

    Python
    167

    crazyhottommy/RNA-seq-analysis

    RNAseq analysis notes from Tommy Tang

    rna-seq snakemake

    Updated Jul 16, 2017

    Python
    125

    COMBINE-lab/salmon

    🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

    c-plus-plus quasi-mapping salmon bioinformatics rna-seq gene-expression rnaseq quantification sailfish

    Updated Jun 2, 2017

    C++
    120

    agitter/single-cell-pseudotime

    An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

    rna-seq single-cell

    Updated Jul 10, 2017

    29

    ndaniel/fusioncatcher

    Finder of Somatic Fusion Genes in RNA-seq data

    somatic-fusion-genes rna-seq fusion-genes

    Updated Jul 14, 2017

    Python
    27

    govinda-kamath/clustering_on_transcript_compatibility_counts

    Clustering cells from single cell RNA seq assays

    paper kallisto rna-seq rna-seq-analysis

    Updated Jul 14, 2017

    Jupyter Notebook
    24

    slowkow/snakefiles

    🐍 Snakefiles for common RNA-seq data analysis workflows.

    snakemake python bioinformatics rna-seq high-performance-computing lsf-jobs

    Updated Jun 30, 2017

    Python
    21

    PF2-pasteur-fr/SARTools

    Statistical Analysis of RNA-Seq Tools

    deseq2 differential-analysis rna-seq r reproducible-research edger

    Updated Jun 13, 2017

    R
    19

    LyonsLab/coge

    CoGe (Comparative Genomics) Platform

    coge perl comparative-genomics python bioinformatics rna-seq genomics synteny genomics-visualization

    Updated Jul 14, 2017

    Perl
    19

    jminnier/STARTapp

    The START App: R Shiny Transcriptome Analysis Resource Tool

    genome-biology shiny visualization bioinformatics rna-seq r transcriptome shiny-apps

    Updated May 14, 2017

    HTML
    18
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