This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

CSSQ

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

Chip-seq Signal Quantifier Pipeline

Bioconductor version: Development (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")

# 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 1.13.1
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License Artistic-2.0
Depends SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer
Imports GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils
Linking To
Suggests BiocStyle, knitr, rmarkdown, markdown
System Requirements
Enhances
URL
See More
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_1.13.1.tar.gz
Windows Binary CSSQ_1.13.1.zip (64-bit only)
macOS Binary (x86_64) CSSQ_1.13.1.tgz
macOS Binary (arm64) CSSQ_1.13.1.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