compartmap

DOI: 10.18129/B9.bioc.compartmap    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see compartmap.

A/B compartment inference from ATAC-seq and methylation array data

Bioconductor version: 3.9

Compartmap performs shrunken A/B compartment inference from ATAC-seq and methylation arrays.

Author: Benjamin Johnson [aut, cre], Tim Triche [aut], Kasper Hansen [aut], Jean-Philippe Fortin [aut]

Maintainer: Benjamin Johnson <ben.johnson at vai.org>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("compartmap")

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("compartmap")

 

HTML	R Script	A/B compartment inference with compartmap
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ATACSeq, Epigenetics, Genetics, ImmunoOncology, MethylSeq, MethylationArray, Software
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL-3 + file LICENSE
Depends	R (>= 3.5.0), minfi, Homo.sapiens, mixOmics
Imports	SummarizedExperiment, GenomicRanges, gtools, parallel
LinkingTo
Suggests	covr, testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/biobenkj/compartmap
BugReports	https://github.com/biobenkj/compartmap/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	compartmap_1.2.0.tar.gz
Windows Binary	compartmap_1.2.0.zip
Mac OS X 10.11 (El Capitan)	compartmap_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/compartmap
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/compartmap
Package Short Url	https://bioconductor.org/packages/compartmap/
Package Downloads Report	Download Stats