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 | ||
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 |