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chromstaR

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data


Bioconductor version: Release (3.18)

This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.

Author: Aaron Taudt, Maria Colome Tatche, Matthias Heinig, Minh Anh Nguyen

Maintainer: Aaron Taudt <aaron.taudt at gmail.com>

Citation (from within R, enter citation("chromstaR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("chromstaR")

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("chromstaR")
The chromstaR user's guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), GenomicRanges, ggplot2, chromstaRData
Imports methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics(>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm
System Requirements
URL https://github.com/ataudt/chromstaR
Bug Reports https://github.com/ataudt/chromstaR/issues
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Suggests knitr, BiocStyle, testthat, biomaRt
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Package Archives

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

Source Package chromstaR_1.28.0.tar.gz
Windows Binary chromstaR_1.28.0.zip
macOS Binary (x86_64) chromstaR_1.28.0.tgz
macOS Binary (arm64) chromstaR_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/chromstaR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chromstaR
Bioc Package Browser https://code.bioconductor.org/browse/chromstaR/
Package Short Url https://bioconductor.org/packages/chromstaR/
Package Downloads Report Download Stats