Bioinformatics Data Analysis Pipeline- ChIP-Seq

DeepTools

Tools for exploring deep sequencing data especially ChIPseq.
Reference: PMID: 27079975
Contact: Qin Ma
MACS2

Transcription factor peak caller for CHIPseq and any other type of DNA enrichment.
Reference: PMID: 18798982
Contact: Qin Ma
ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data.
Reference: PMID: 20459804
Contact: Qin Ma
DiffBind

Differential Binding Analysis of ChIP-Seq Peak Data.
Reference: PMID: 25972895
Contact: Qin Ma
HOMER

Software for motif discovery and next-gen sequencing analysis.
Reference: PMID: 20513432
Contact: Qin Ma