HiCDOC

DOI: 10.18129/B9.bioc.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 (3.17)

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>

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

Installation

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

 

HTML R Script HiCDOC
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DNA3DStructure, HiC, Normalization, Sequencing, Software
Version 1.1.1
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package HiCDOC_1.1.1.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiCDOC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCDOC
Package Short Url https://bioconductor.org/packages/HiCDOC/
Package Downloads Report Download Stats

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