chromstaR

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see chromstaR.

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data


Bioconductor version: 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
See More
Suggests knitr, BiocStyle, testthat, biomaRt
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 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