CSAR
This is the released version of CSAR; for the devel version, see CSAR.
Statistical tools for the analysis of ChIP-seq data
Bioconductor version: Release (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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.64.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (16.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | CSAR_1.64.0.tar.gz |
| Windows Binary (x86_64) | CSAR_1.64.0.zip |
| macOS Binary (big-sur-x86_64) | CSAR_1.64.0.tgz |
| macOS Binary (sonoma-arm64) | CSAR_1.64.0.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 |