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HiCDOC

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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HiCDOC")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HiCDOC")
HiCDOC HTML R Script
Reference Manual PDF
NEWS Text

Details

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
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
Linking To Rcpp
Enhances
Depends On Me
Imports Me treediff
Suggests Me
Links To Me
Build Report Build Report

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/
Package Downloads Report Download Stats