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ChIA-PET data analysis bioinformatics software tools

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 analysis steps

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WashU…
Web

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.…

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R3CPET
Desktop

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,…

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ChIA-PET
Desktop

ChIA-PET

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-PET can detect chromatin…

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QuIN
Web
Desktop

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…

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PET-Tool
Web

PET-Tool Paired End ditag tool

Allows users to process and manage the Paired End diTag (PET) data generated…

Allows users to process and manage the Paired End diTag (PET) data generated from GIS-PET and ChIP-PET experiments. Pet-Tool is a web application is composed of four components : (i) ProjectManager…

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Mango
Desktop

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…

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GenomicInteract…
Desktop

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…

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ChiaSig
Desktop

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…

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Lollipop
Desktop

Lollipop

Assists in making genome-wide predictions of CCCTC-binding factor…

Assists in making genome-wide predictions of CCCTC-binding factor (CTCF)-mediated loops. Lollipop is a machine-learning framework based on random forests classifier. It accounts for the complexity of…

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Pgltools
Desktop

Pgltools

Uses for interacting with the PGL file standard for paired-genomic loci.…

Uses for interacting with the PGL file standard for paired-genomic loci. Pgltools is a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python…

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MICC
Desktop

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…

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MDM
Desktop

MDM

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. MDM provides: (i) a function MCDIST to detect ture chromatin…

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ChIA-PET Tool
Desktop

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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