HiCDOC

DOI: 10.18129/B9.bioc.HiCDOC  

A/B compartment detection and differential analysis

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

HTML	R Script	HiCDOC
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DNA3DStructure, HiC, Normalization, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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, rhdf5, grid, ggpubr, gridExtra, ggExtra, data.table, multiHiCcompare, GenomeInfoDb
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, testthat, BiocStyle, BiocManager
SystemRequirements	C++11
Enhances
URL	https://github.com/mzytnicki/HiCDOC
BugReports	https://github.com/mzytnicki/HiCDOC/issues
Depends On Me
Imports Me	treediff
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiCDOC_1.2.0.tar.gz
Windows Binary	HiCDOC_1.2.0.zip (64-bit only)
macOS Binary (x86_64)	HiCDOC_1.2.0.tgz
macOS Binary (arm64)	HiCDOC_1.2.0.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
Old Source Packages for BioC 3.17	Source Archive