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Contact matrix normalization 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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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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HiCapp
Desktop

HiCapp HiCorrectorapp

Corrects the copy number bias in tumor HiCorrector (Hi-C) data using…

Corrects the copy number bias in tumor HiCorrector (Hi-C) data using chromosome-adjusted iterative correction bias (caICB) correction algorithm. HiCapp is able to efficiently correct for the copy…

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HiCNorm
Desktop

HiCNorm

A parametric model to remove systematic biases in the raw Hi-C contact maps,…

A parametric model to remove systematic biases in the raw Hi-C contact maps, resulting in a simple, fast, yet accurate normalization procedure.

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bnbc
Desktop

bnbc bandwise normalization and batch correction

Allows users to normalize and batch correct Hi-C data from replicates. Bnbc is…

Allows users to normalize and batch correct Hi-C data from replicates. Bnbc is a R package that provides a cross-sample approach that preserves Hi-C contact maps, stabilizes the marginal…

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HiCcompare
Desktop

HiCcompare

Allows joint normalization and difference detection in multiple chromosome…

Allows joint normalization and difference detection in multiple chromosome conformation capture sequencing technologies (Hi-C) datasets. HiCcompare is an extension of the popular RNA-seq differential…

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HiFive
Desktop
Web

HiFive

A set of tools for handling HiC and 5C data. HiFive provides efficient data…

A set of tools for handling HiC and 5C data. HiFive provides efficient data handling and a variety of normalization approaches for easy, fast analysis and method comparison. Integration of MPI-based…

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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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HiCdat
Desktop

HiCdat

Provides a simple graphical user interface for data pre-processing and a…

Provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional…

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Binless
Desktop

Binless

Permits normalization of 3C-like data. Binless is able to compute matrices that…

Permits normalization of 3C-like data. Binless is able to compute matrices that adapt to the size of the features present in the data. It aims to take genomic and polymer effects out of the data.…

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cancer-hic-norm
Desktop

cancer-hic-norm

Explores the impact of copy number variants (CNVs) on Hi-C data.…

Explores the impact of copy number variants (CNVs) on Hi-C data. cancer-hic-norm provides a solution to deal with its effect on cancer data normalization. This tool proposes a model simulating large…

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Dryhic
Desktop

Dryhic

Corrects local chromosomal abnormalities in Hi-C experiments. Dryhic is a set…

Corrects local chromosomal abnormalities in Hi-C experiments. Dryhic is a set of tools that was developed ground up to address the need to normalize data from biological samples with aberrant…

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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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HiCorrector
Desktop

HiCorrector

An easy-to-use, open source implementation of the Hi-C data normalization…

An easy-to-use, open source implementation of the Hi-C data normalization algorithm. Its salient features are (i) scalability - the software is capable of normalizing Hi-C data of any size in…

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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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