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CSAR
This is thedevelopment version of CSAR; for the stable release version, seeCSAR.
Statistical tools for the analysis of ChIP-seq data
Bioconductor version: Development (3.23)
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 "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("CSAR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.63.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15.0),S4Vectors,IRanges,Seqinfo,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
FollowInstallation instructions to use this package in your R session.
| Source Package | CSAR_1.63.0.tar.gz |
| Windows Binary (x86_64) | CSAR_1.63.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | CSAR_1.63.0.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 |