CSSQ

DOI: 10.18129/B9.bioc.CSSQ    

Chip-seq Signal Quantifier Pipeline

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	Introduction to CSSQ
PDF		Reference Manual

Details

biocViews	ChIPSeq, DifferentialPeakCalling, Normalization, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.11 (R-4.0) (2 years)
License	Artistic-2.0
Depends	SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer
Imports	GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, markdown
SystemRequirements
Enhances
URL
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	CSSQ_1.6.0.tar.gz
Windows Binary	CSSQ_1.6.0.zip
macOS 10.13 (High Sierra)	CSSQ_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CSSQ
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CSSQ
Package Short Url	https://bioconductor.org/packages/CSSQ/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive