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CodeSpringLab

Collection of bioinformatics pipelines and scripts for Cold Spring Harbor Laboratory created by BSR (Bioinformatics shared resources)

Highlights

  1. Bulk RNA-seq:

    FastQC and fastq-screen

    Cutadapt

    STAR and Kallisto

    featureCounts and RSEM

    DESeq2

    GSEApy

    PCA, Heatmap, Volcano, and MA plots

  2. Bulk ATAC-seq:

    FastQC and fastq-screen

    Cutadapt

    Bowtie2

    MACS2

    DiffBind

    Homer, Picard, SAMtools, and deepTools

    Profile map, PCA, Heatmap, Volcano, and Box plots

  3. Bulk ChIP-seq:

    FastQC and fastq-screen

    Cutadapt

    Bowtie2

    MACS2

    DiffBind

    Homer, Picard, SAMtools, and deepTools

    Profile map, PCA, Heatmap, Volcano, and Box plots