CSSQ
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CSSQ.
Chip-seq Signal Quantifier Pipeline
Bioconductor version: 3.13
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("CSSQ")
):
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")
Introduction to CSSQ | HTML | R Script |
Reference Manual |
Details
biocViews | ChIPSeq, DifferentialPeakCalling, Normalization, Sequencing, Software |
Version | 1.4.1 |
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 | |
URL |
See More
Suggests | BiocStyle, knitr, rmarkdown, markdown |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | CSSQ_1.4.1.tar.gz |
Windows Binary | CSSQ_1.4.1.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | CSSQ_1.4.1.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 |
Old Source Packages for BioC 3.13 | Source Archive |