CSSQ
Chip-seq Signal Quantifier Pipeline
Bioconductor version: Release (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 <yuhong.fan at biology.gatech.edu>
Citation (from within R, enter
citation("CSSQ")):
Installation
To install this package, start R (version "4.4") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | CSSQ_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | CSSQ_1.18.0.tgz |
| macOS Binary (arm64) | CSSQ_1.18.0.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 |