ChIP-seq Tools

This package implements functions to retrieve the nearest genes around the peak, annotate the genomic region of the peak, statistical methods for estimating the significance of overlap among ChIP peak data sets, and incorporate GEO database to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses.

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Peak finder for NGS datasets that can integrate replicates and assign peak boundaries accurately.

Model based analysis for chip-seq data

A supervised learning framework for chromatin loop detection in genome-wide contact maps. It can be used to visualize Hi-C, ChIA-PET, HiCHiP, PLAC-Seq, Capture Hi-C data.

A clustering approach for identification of enriched domains from histone modification ChIP-seq data.