chromstaR

DOI: 10.18129/B9.bioc.chromstaR    

This is the development version of chromstaR; for the stable release version, see chromstaR.

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("chromstaR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.4 (R-3.3) (5 years)
License Artistic-2.0
Depends R (>= 3.3), GenomicRanges, ggplot2, chromstaRData
Imports methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics(>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, reshape2, Rsamtools, GenomicAlignments, bamsignals, mvtnorm
LinkingTo
Suggests knitr, BiocStyle, testthat, biomaRt
SystemRequirements
Enhances
URL https://github.com/ataudt/chromstaR
BugReports https://github.com/ataudt/chromstaR/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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/chromstaR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/chromstaR
Package Short Url https://bioconductor.org/packages/chromstaR/
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