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CSSQ

Chip-seq Signal Quantifier Pipeline


Bioconductor version: Release (3.18)

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

Author: Ashwath Kumar [aut], Michael Y Hu [aut], Yajun Mei [aut], Yuhong Fan [aut]

Maintainer: Fan Lab at Georgia Institute of Technology <yuhong.fan at biology.gatech.edu>

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

Installation

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


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

BiocManager::install("CSSQ")

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("CSSQ")
Introduction to CSSQ HTML R Script
Reference Manual PDF

Details

biocViews ChIPSeq, DifferentialPeakCalling, Normalization, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License Artistic-2.0
Depends SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer
Imports GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils
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Suggests BiocStyle, knitr, rmarkdown, markdown
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Package Archives

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

Source Package CSSQ_1.14.0.tar.gz
Windows Binary CSSQ_1.14.0.zip
macOS Binary (x86_64) CSSQ_1.14.0.tgz
macOS Binary (arm64) CSSQ_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CSSQ
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CSSQ
Bioc Package Browser https://code.bioconductor.org/browse/CSSQ/
Package Short Url https://bioconductor.org/packages/CSSQ/
Package Downloads Report Download Stats