chromswitch
This package is for version 3.14 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: 3.14
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("chromswitch")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DifferentialPeakCalling, Epigenetics, FunctionalGenomics, GeneExpression, HistoneModification, ImmunoOncology, MultipleComparison, Software, Transcription |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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) |
| System Requirements | |
| URL | https://github.com/sjessa/chromswitch |
| Bug Reports | https://github.com/sjessa/chromswitch/issues |
See More
| Suggests | BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb(>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | chromswitch_1.16.0.tar.gz |
| Windows Binary | chromswitch_1.16.0.zip |
| macOS 10.13 (High Sierra) | chromswitch_1.16.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |