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

Chip-seq Signal Quantifier Pipeline

Bioconductor version: Development (3.20)

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 < at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to CSSQ HTML R Script
Reference Manual PDF


biocViews ChIPSeq, DifferentialPeakCalling, Normalization, Sequencing, Software
Version 1.17.0
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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Follow Installation instructions to use this package in your R session.

Source Package CSSQ_1.17.0.tar.gz
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macOS Binary (x86_64) CSSQ_1.17.0.tgz
macOS Binary (arm64) CSSQ_1.17.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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