chromswitch

DOI: 10.18129/B9.bioc.chromswitch  

An R package to detect chromatin state switches from epigenomic data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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_1.20.0.tar.gz
Windows Binary	chromswitch_1.20.0.zip
macOS Binary (x86_64)	chromswitch_1.20.0.tgz
macOS Binary (arm64)	chromswitch_1.20.0.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