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Contact matrix generation software tools | Hi-C data analysis

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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HiTC
Desktop

HiTC

Facilitates the exploration of high-throughput 3C-based data. HiTC allows users…

Facilitates the exploration of high-throughput 3C-based data. HiTC allows users to import and export ‘C’ data, to transform, normalize, annotate and visualize interaction maps. It proposes a…

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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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ICE
Desktop

ICE Iterative Correction and Eigenvector decomposition

A computational pipeline that integrates a strategy to map sequencing reads…

A computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities.…

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Hicpipe
Desktop

Hicpipe Hi-C Pipeline

A probabilistic model for Hi-C data and explore chromosomal architectures in…

A probabilistic model for Hi-C data and explore chromosomal architectures in human lymphoblasts using it. Hicpipe is a set of scripts and programs that correct Hi-C contact maps, given a list…

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hiclib
Desktop

hiclib

Maps, filters and analyzes Hi-C data. hiclib integrates a strategy to map…

Maps, filters and analyzes Hi-C data. hiclib integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact…

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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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HiCExplorer
Desktop

HiCExplorer

Simplifies the Hi-C data pre-processing, contact matrix transformation, and…

Simplifies the Hi-C data pre-processing, contact matrix transformation, and topologically associating domain (TAD) calling into a few easy steps. HiCExplorer is a tool-suite that can be used with…

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HiC-Pro
Desktop

HiC-Pro

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data)…

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. The pipeline is flexible, scalable and optimized. It can operate either on a single…

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TADbit
Desktop

TADbit

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational…

Allows analysis and 3D modelling of 3C-based data. TADbit is a computational framework including: (i) read quality control and design of the mapping strategy; (ii) mapping of reads to the reference…

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hiCtools
Desktop

hiCtools

This collection of tools stream-lines the processing of HiC data from raw…

This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond.

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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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