CSAR
Statistical tools for the analysis of ChIP-seq data
Bioconductor version: Release (3.20)
Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.
Author: Jose M Muino
Maintainer: Jose M Muino <jose.muino at live.com>
citation("CSAR")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CSAR")
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("CSAR")| CSAR Vignette | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, Genetics, Software, Transcription |
| Version | 1.58.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (14.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges |
| Imports | stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | ShortRead, Biostrings |
| 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 | CSAR_1.58.0.tar.gz |
| Windows Binary (x86_64) | CSAR_1.58.0.zip |
| macOS Binary (x86_64) | CSAR_1.58.0.tgz |
| macOS Binary (arm64) | CSAR_1.57.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CSAR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CSAR |
| Bioc Package Browser | https://code.bioconductor.org/browse/CSAR/ |
| Package Short Url | https://bioconductor.org/packages/CSAR/ |
| Package Downloads Report | Download Stats |