chromswitch

DOI: 10.18129/B9.bioc.chromswitch    

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

An R package to detect chromatin state switches from epigenomic data

Bioconductor version: Development (3.11)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, ImmunoOncology, MultipleComparison, Software, Transcription
Version 1.9.0
In Bioconductor since BioC 3.6 (R-3.4) (2 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), 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(>= 0.23.19), stats, tidyr (>= 0.6.3)
LinkingTo
Suggests BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb(>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat
SystemRequirements
Enhances
URL https://github.com/sjessa/chromswitch
BugReports https://github.com/sjessa/chromswitch/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 chromswitch_1.9.0.tar.gz
Windows Binary chromswitch_1.9.0.zip
Mac OS X 10.11 (El Capitan) chromswitch_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chromswitch
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chromswitch
Package Short Url https://bioconductor.org/packages/chromswitch/
Package Downloads Report Download Stats

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