CSAR
Statistical tools for the analysis of ChIP-seq data
Bioconductor version: 2.9
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 wur.nl>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("CSAR")
To cite this package in a publication, start R and enter:
citation("CSAR")
Documentation
| R Script | CSAR Vignette | |
| Reference Manual |
Details
| biocViews | ChIPseq, Transcription, Genetics |
| Depends | R(>= 2.6.0) |
| Imports | stats, utils |
| Suggests | ShortRead, Biostrings |
| System Requirements | |
| License | Artistic-2.0 |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 1.6.0 |
| Since | Bioconductor 2.6 (R-2.11) |
Package Downloads
| Package Source | CSAR_1.6.0.tar.gz |
| Windows Binary | CSAR_1.6.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | CSAR_1.6.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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