compartmap

DOI: 10.18129/B9.bioc.compartmap    

This is the development version of compartmap; for the stable release version, see compartmap.

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

Bioconductor version: Development (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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("compartmap", version = "3.9")

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, MethylSeq, MethylationArray, Software
Version 1.1.0
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_1.1.0.tar.gz
Windows Binary compartmap_1.1.0.zip
Mac OS X 10.11 (El Capitan) compartmap_1.1.0.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 http://bioconductor.org/packages/compartmap/
Package Downloads Report Download Stats

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