ChIP sequencing data analysis software tools

Chromatin immunoprecipitation followed by sequencing (ChIP-seq), first described in 2007 (Barski et al., 2007; Johnson et al., 2007; Mikkelsen et al., 2007; Robertson et al., 2007), allows in vivo determination of where a protein binds the genome, which can be transcription factors, DNA-binding enzymes, histones, chaperones, or nucleosomes (Park, 2009; Furey, 2012).

DNA-Protein interactions

Data preprocessing

Data processing

Data analysis


Protein sequence/Expression


Data visualization

Network analysis

Enrichment analysis

Integrative analysis


File manipulation


Unclassified tools