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 (3.17)

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 "4.3") and enter:

if (!require("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

Details

biocViews	Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, ImmunoOncology, MultipleComparison, Software, Transcription
Version	1.21.0
In Bioconductor since	BioC 3.6 (R-3.4) (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
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Build Report

Package Archives

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

Source Package	chromswitch_1.21.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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