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Workflow software tools | Hi-C data analysis

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scell_hicpipe
Desktop

scell_hicpipe Single cell Hi-C Pipeline

Allows users to identify thousands of simultaneous chromatin contacts in a…

Allows users to identify thousands of simultaneous chromatin contacts in a single cell. The Single cell Hi-C Pipeline consists in a set of scripts that process single cell Hi-C libraries. It is able…

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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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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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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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GAMtools
Desktop

GAMtools

Analyzes Genome Architecture Mapping (GAM) datasets. GAMtools covers the…

Analyzes Genome Architecture Mapping (GAM) datasets. GAMtools covers the automated mapping of raw next-generation sequencing (NGS) data generated by GAM, detection of genomic regions present in each…

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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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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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AutoChrom3D
Desktop
Web

AutoChrom3D

An approach for chromatin structure prediction capable of relaxing both kinds…

An approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line…

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HBP
Desktop

HBP Hi-C BED file analysis Pipeline

Integrates existing pipelines focusing on individual steps of Hi-C data…

Integrates existing pipelines focusing on individual steps of Hi-C data processing into an all-in-one package with adjustable parameters to infer the consensus 3D structure of genome from raw Hi-C…

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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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Hi.C
Desktop

Hi.C

Provides a Hi-C pipeline written in C. Hi.C is an application that generates…

Provides a Hi-C pipeline written in C. Hi.C is an application that generates three binaries: (i) an in-silico digestion of genomes using defined restriction enzymes, (ii) reads mapped files and finds…

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HiCUP
Desktop

HiCUP Hi-C User Pipeline

A tool for mapping and performing quality control on Hi-C data. HiCUP is…

A tool for mapping and performing quality control on Hi-C data. HiCUP is designed to take the raw sequence output from a HiC experiment and produce a filtered set of mapped interaction pairs,…

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