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This is the development version of HiCDOC; for the stable release version, see HiCDOC.

A/B compartment detection and differential analysis

Bioconductor version: Development (3.19)

HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.

Author: Kurylo Cyril [aut], Zytnicki Matthias [aut], Foissac Sylvain [aut], Maigné Élise [aut, cre]

Maintainer: Maigné Élise <elise.maigne at inrae.fr>

Citation (from within R, enter citation("HiCDOC")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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Reference Manual PDF


biocViews Clustering, DNA3DStructure, HiC, Normalization, Sequencing, Software
Version 1.5.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License LGPL-3
Depends InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0)
Imports methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb
System Requirements C++11
URL https://github.com/mzytnicki/HiCDOC
Bug Reports https://github.com/mzytnicki/HiCDOC/issues
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Suggests knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
Linking To Rcpp
Depends On Me
Imports Me treediff
Suggests Me
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiCDOC_1.5.1.tar.gz
Windows Binary HiCDOC_1.5.1.zip
macOS Binary (x86_64) HiCDOC_1.5.1.tgz
macOS Binary (arm64) HiCDOC_1.5.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCDOC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCDOC
Bioc Package Browser https://code.bioconductor.org/browse/HiCDOC/
Package Short Url https://bioconductor.org/packages/HiCDOC/
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