chromstaR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see chromstaR.

Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

DOI: 10.18129/B9.bioc.chromstaR

Bioconductor version: 3.21

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 "4.5") 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

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, ChIPSeq, DifferentialPeakCalling, HiddenMarkovModel, HistoneModification, ImmunoOncology, MultipleComparison, PeakDetection, Sequencing, Software

Version 1.34.0

In Bioconductor since BioC 3.4 (R-3.3) (9 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

System Requirements

URL https://github.com/ataudt/chromstaR

Bug Reports https://github.com/ataudt/chromstaR/issues

Suggests knitr, BiocStyle, testthat, biomaRt

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Package Archives

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

Source Package

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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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