diffNGS: differential peak analysis in Next-Generation Sequencing data with replicates

diffNGS is a modified version of function narrowpeaksDiff.R of the Bioconductor package NarrowPeaks: Shape-based Analysis of Variation in ChIP-seq using Functional PCA.

The repository contains an R script that can be used to identify differential read-enriched regions in normalized bigwig files obtained from replicated ATAC-seq/DNase-seq/ChIP-seq data. Peak calling at each condition and generation of normalized bigwig tracks of the samples should be done before using diffNGS.

Examples

for ATAC-seq

https://github.com/pmb59/endoderm/tree/master/atacseq/diffNGS

for ChIP-seq

An application of the package for Arabidopsis datasets is described here.

Citation

Please cite this paper if you use diffNGS in your research:

Mateos JL, Madrigal P, et al. Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biology 16, 31 (2015).