Code Repository for Paper : NSD2 is a requisite subunit of the AR/FOXA1 neo-enhanceosome in promoting prostate tumorigenesis
Paper Citation goes here.
Repo Contents
RNA-Seq
Run_RNAseq_kallisto.sh - basic pseudo alignment
bulkRNA_Rscripts.R - R >3.6.0, additional analysis on bulk RNA data, GSEA, volcano outputs
ChIP-Seq
ChipAlignment_PE.sh - Basic alignment paired end pipeline (bwamem, samtools, picard wrapper)
EnrichmentHeatmaps.sh - Uses Deeptools to create heatmaps
OverlapCompare.R - Uses R>3.6.0 to implement a combination of ChipPeakAnno and ChipSeeker packages to compare output from MACS peak calling
Run_HOMER.sh - Runs HOMER motif analysis
TrackPlot.R - Uses R> 4.0.1 and R package Sushi to generate IGV style tracks with labeled motifs.
Copy of version information for software/tools needed to run these. Cites.