chromswitch

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see chromswitch.

An R package to detect chromatin state switches from epigenomic data


Bioconductor version: 3.9

Chromswitch implements a flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP-seq data.

Author: Selin Jessa [aut, cre], Claudia L. Kleinman [aut]

Maintainer: Selin Jessa <selinjessa at gmail.com>

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

Installation

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


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

BiocManager::install("chromswitch")

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("chromswitch")
An introduction to `chromswitch` for detecting chromatin state switches HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, ImmunoOncology, MultipleComparison, Software, Transcription
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License MIT + file LICENSE
Depends R (>= 3.4), GenomicRanges(>= 1.26.4)
Imports cluster (>= 2.0.6), Biobase(>= 2.36.2), BiocParallel(>= 1.8.2), dplyr (>= 0.5.0), gplots (>= 3.0.1), graphics, grDevices, IRanges(>= 2.4.8), lazyeval (>= 0.2.0), matrixStats (>= 0.52), magrittr (>= 1.5), methods, NMF (>= 0.20.6), rtracklayer(>= 1.36.4), S4Vectors(>= 0.14.4), stats, tidyr (>= 0.6.3)
System Requirements
URL https://github.com/sjessa/chromswitch
Bug Reports https://github.com/sjessa/chromswitch/issues
See More
Suggests BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb(>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat
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Package Archives

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

Source Package chromswitch_1.6.0.tar.gz
Windows Binary chromswitch_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) chromswitch_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chromswitch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chromswitch
Bioc Package Browser https://code.bioconductor.org/browse/chromswitch/
Package Short Url https://bioconductor.org/packages/chromswitch/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive