CSAR: Statistical tools for the analysis of ChIP-seq data

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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
Date of publication
None
Maintainer
Jose M Muino <jose.muino@wur.nl>
License
Artistic-2.0
Version
1.26.0

View on Bioconductor

Man pages

ChIPseqScore
Calculate read-enrichment scores for each nucleotide position
CSAR-package
Statistical tools for the analysis of ChIP-seq data
distance2Genes
Calculate relative positions of read-enriched regions...
genesWithPeaks
Provide table of genes with read-enriched regions, and their...
getPermutatedWinScores
Obtain the read-enrichment score distribution under the null...
getThreshold
Calculate the threshold value corresponding to control FDR at...
loadMappedReads
Load mapped reads
mappedReads2Nhits
Calculate number of overlapped extended reads per nucleotide...
permutatedWinScores
Calculate scores for permutated read-enriched regions
sampleSEP3_test
Partial dataset of a ChIP-seq experiment
score2wig
Save the read-enrichment scores at each nucleotide position...
sigWin
Calculate regions of read-enrichment

Files in this package

CSAR/DESCRIPTION
CSAR/NAMESPACE
CSAR/R
CSAR/R/ChIPseqScore.R
CSAR/R/LoadBinCSAR.R
CSAR/R/distance2Genes.R
CSAR/R/genesWithPeaks.R
CSAR/R/getPermutatedWinScores.R
CSAR/R/getThreshold.R
CSAR/R/loadMappedReads.R
CSAR/R/mappedReads2Nhits.R
CSAR/R/mappedReads2Nhits_chr.R
CSAR/R/permutatedWinScores.R
CSAR/R/pos2Nhits.R
CSAR/R/score2wig.R
CSAR/R/score_chr.R
CSAR/R/sigWin.R
CSAR/R/sigWin_chr.R
CSAR/build
CSAR/build/vignette.rds
CSAR/data
CSAR/data/CSAR-dataset.rda
CSAR/inst
CSAR/inst/CITATION
CSAR/inst/doc
CSAR/inst/doc/CSAR.R
CSAR/inst/doc/CSAR.Rnw
CSAR/inst/doc/CSAR.pdf
CSAR/man
CSAR/man/CSAR-package.Rd
CSAR/man/ChIPseqScore.Rd
CSAR/man/distance2Genes.Rd
CSAR/man/genesWithPeaks.Rd
CSAR/man/getPermutatedWinScores.Rd
CSAR/man/getThreshold.Rd
CSAR/man/loadMappedReads.Rd
CSAR/man/mappedReads2Nhits.Rd
CSAR/man/permutatedWinScores.Rd
CSAR/man/sampleSEP3_test.Rd
CSAR/man/score2wig.Rd
CSAR/man/sigWin.Rd
CSAR/src
CSAR/src/CSAR.c
CSAR/src/CSAR.h
CSAR/vignettes
CSAR/vignettes/CSAR.Rnw
CSAR/vignettes/CSARVignette.bib