Tools
homer
GPL-3.0-or-later
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
samtools
MIT
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.
DESeq2
LGPL-3.0-or-later
Differential gene expression analysis based on the negative binomial distribution
edgeR
GPL >=2
Empirical Analysis of Digital Gene Expression Data in R