ChIA-PET data analysis bioinformatics software tools

ChIA-PET analysis steps

A number of high-throughput methods based on nuclear proximity ligation have been developed to detect genome-wide chromatin interactions, including high-throughput chromosome conformation capture (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET)…

ChIA-PET data analysis bioinformatics software tools

Web app
G T A T C G C T A WashU Epigenome… WashU Epigenome Browser

WashU Epigenome Browser

A genome browser focusing on the human epigenome. The Browser is web-based and…

A genome browser focusing on the human epigenome. The Browser is web-based and it extends the seminal concept invented by the UCSC Cancer Genomics Browser to support large, sequencing-based datasets.…

Web app
Desktop app
G T A T C G C T A Query tool for… Query tool for Interaction Networks

QuIN Query tool for Interaction Networks

A web-based application for visualizing, annotating, and querying chromatin…

A web-based application for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC. QuIN enables: 1) building and visualizing chromatin…

Desktop app
G T A T C G C T A R3CPET R3CPET

R3CPET

An R package based on a non-parametric Bayesian approach, to infer the set of…

An R package based on a non-parametric Bayesian approach, to infer the set of the most probable protein complexes involved in maintaining chromatin interactions and the regions that they may control,…

Desktop app
G T A T C G C T A GenomicInteractions GenomicInteractions

GenomicInteractions

An R/Bioconductor package for the manipulation, annotation and visualisation of…

An R/Bioconductor package for the manipulation, annotation and visualisation of various types of chromatin interaction data, e.g. Hi-C, ChIA-PET. GenomicInteractions allows the easy annotation and…

Desktop app
G T A T C G C T A MCDIST MCDIST

MCDIST

Offers functions for the analysis of chromatin interactions using MC_DIST model…

Offers functions for the analysis of chromatin interactions using MC_DIST model (one sample problem), Two-Step model and One-Step model. MCDIST provides: (i) a function MCDIST to detect ture…

Desktop app
G T A T C G C T A ChIA-PET2 ChIA-PET2

ChIA-PET2

An easy-to-use and complete analysis pipeline to process both bridge-linker and…

An easy-to-use and complete analysis pipeline to process both bridge-linker and half-linker ChIA-PET data from raw sequencing reads to significant chromatin loop calls. ChIA-PET2 can detect chromatin…

Desktop app
G T A T C G C T A Model based… Model based Interaction Calling from ChIA-PET data

MICC Model based Interaction Calling from ChIA-PET data

An easy-to-use R package to detect chromatin interactions from ChIA-PET…

An easy-to-use R package to detect chromatin interactions from ChIA-PET sequencing data. By applying a Bayesian mixture model to systematically remove random ligation and random collision noise, MICC…

Desktop app
G T A T C G C T A Mango Mango

Mango

A complete ChIA-PET data analysis pipeline that provides statistical confidence…

A complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic…

Desktop app
G T A T C G C T A ChiaSig ChiaSig

ChiaSig

A statistical test for detection of significant interactions between genomic…

A statistical test for detection of significant interactions between genomic elements in ChIA-PET datasets, applying the non-central hypergeometric (NCHG) distribution. Unlike previous methods, our…

Desktop app
G T A T C G C T A MDM (formerly MCDIST) MDM (formerly MCDIST)

MDM (formerly MCDIST)

Provides functions for the analysis of chromatin interactions using MC_DIST…

Provides functions for the analysis of chromatin interactions using MC_DIST model (for one sample problem, i.e., detecting chromatin interactions from noises), Two-Step model and One-Step model (for…

Desktop app
G T A T C G C T A ChIA-PET Tool ChIA-PET Tool

ChIA-PET Tool

A software package for automatic processing of ChIA-PET sequence data,…

A software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and…

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