ChIP sequencing data analysis software tools

ChIP sequencing data analysis software tools Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is a genomics and epigenomics method to study DNA-protein interactions. ChIP-sequencing uses antibodies that are specific to a protein of interest combined with high-throughput sequencing to map every protein-binding site on a given genome. This method is widely used for the discovery of new regulatory elements such as transcription factors and histone modifications. ChIP-seq data analysis software are essential for data pre-processing and processing (quality control, read alignment, etc.), data analysis, annotation, data visualization and network analysis.

DNA-Protein interactions

Data preprocessing

Data processing


Data analysis


Data visualization

Network analysis

Enrichment analysis

Integrative analysis


File manipulation


Unclassified tools