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>

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

Installation

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


if (!require("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")
A/B compartment inference with compartmap HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ATACSeq, Epigenetics, Genetics, ImmunoOncology, MethylSeq, MethylationArray, Software
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-3 + file LICENSE
Depends R (>= 3.5.0), minfi, Homo.sapiens, mixOmics
Imports SummarizedExperiment, GenomicRanges, gtools, parallel
System Requirements
URL https://github.com/biobenkj/compartmap
Bug Reports https://github.com/biobenkj/compartmap/issues
See More
Suggests covr, testthat, knitr
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Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/compartmap/
Package Short Url https://bioconductor.org/packages/compartmap/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive