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CSSQ

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

Chip-seq Signal Quantifier Pipeline


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

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

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 1.15.0
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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, markdown
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Build Report Build Report

Package Archives

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

Source Package CSSQ_1.15.0.tar.gz
Windows Binary CSSQ_1.15.0.zip (64-bit only)
macOS Binary (x86_64) CSSQ_1.15.0.tgz
macOS Binary (arm64) CSSQ_1.15.0.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