CSSQ

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11

Chip-seq Signal Quantifier Pipeline

Bioconductor version: Development (3.24)

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")):

Ashwath Kumar, Michael Y Hu, Yajun Mei, Yuhong Fan. CSSQ: Chip-seq Signal Quantifier Pipeline. doi:10.18129/B9.bioc.CSSQ, R package version 1.25.0, https://bioconductor.org/packages/CSSQ.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, DifferentialPeakCalling, Normalization, Sequencing, Software
Version	1.25.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
License	Artistic-2.0
Depends	SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, rtracklayer
Imports	GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2, grDevices, stats, utils
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, markdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	CSSQ_1.25.0.tar.gz
Windows Binary (x86_64)	CSSQ_1.25.0.zip
macOS Binary (big-sur-x86_64)	CSSQ_1.25.0.tgz
macOS Binary (sonoma-arm64)	CSSQ_1.25.0.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