chromswitch

This package is for version 3.7 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

DOI: 10.18129/B9.bioc.chromswitch

Bioconductor version: 3.7

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 "3.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, MultipleComparison, Software, Transcription

Version 1.2.1

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

Suggests BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb(>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat

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