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Peak calling software tools | Hi-C data analysis

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Juicer
Desktop

Juicer

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a…

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file…

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Fit-Hi-C
Desktop

Fit-Hi-C

A tool for assigning statistical confidence estimates to intra-chromosomal…

A tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

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FastHiC
Desktop

FastHiC

A hidden Markov random field (HMRF)-based peak caller to detect long-range…

A hidden Markov random field (HMRF)-based peak caller to detect long-range chromosomal interactions from Hi-C data. In real Hi-C data analysis, FastHiC runs around ten times faster than our previous…

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GOTHiC
Desktop

GOTHiC

Detects the spatial proximity between pairs of genomic loci. GOTHiC is a…

Detects the spatial proximity between pairs of genomic loci. GOTHiC is a binomial model that corrects the complex combination of known and unknown biases in Hi-C data by assuming that all biases are…

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HubPredictor
Desktop

HubPredictor

A computational model integrating Hi-C and histone mark ChIP-seq data to…

A computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD)…

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HMRFBayesHiC
Desktop

HMRFBayesHiC

A hidden Markov random field based Bayesian peak caller to identify long range…

A hidden Markov random field based Bayesian peak caller to identify long range chromatin interactions from Hi-C data. Comparing to the existing anchor-fragment peak caller, HMRFBayesHiC is the first…

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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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chromoR
Desktop

chromoR

Provides users with a statistical pipeline for analysing chromosomal…

Provides users with a statistical pipeline for analysing chromosomal interactions data (Hi-C data). chromoR combines wavelet methods and a Bayesian approach for correction (bias and noise) and…

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HIPPIE
Desktop
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ChromContact
Web

ChromContact

A web server for analyzing spatial contact of chromosomes from the publicly…

A web server for analyzing spatial contact of chromosomes from the publicly available Hi-C data. ChromContact is designed to be simple and easy to use. By specifying a locus of interest, ChromContact…

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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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HiC-inspector
Desktop

HiC-inspector

A bioinformatics pipeline for the automated analysis of data generated by…

A bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome…

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