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