chromswitch

DOI: 10.18129/B9.bioc.chromswitch  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 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: Release (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")

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	1.22.0
In Bioconductor since	BioC 3.6 (R-3.4) (6 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_1.22.0.tar.gz
Windows Binary	chromswitch_1.22.0.zip (64-bit only)
macOS Binary (x86_64)	chromswitch_1.22.0.tgz
macOS Binary (arm64)	chromswitch_1.22.0.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
Old Source Packages for BioC 3.17	Source Archive