Statistical tools for ChIP-seq data analysis.
The package is oriented to plant organisms, and compatible with standard file formats in the plant research field.
● Data Source:
BioConductor
● Keywords:
● Alias: CSAR-package
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ChIPseqScore
(Package: CSAR) :
Calculate read-enrichment scores for each nucleotide position
Calculate read-enrichment scores for each nucleotide position
● Data Source:
BioConductor
● Keywords:
● Alias: ChIPseqScore, score_chr
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distance2Genes
(Package: CSAR) :
Calculate relative positions of read-enriched regions regarding gene position
Calculate relative positions of read-enrichment regions regarding gene position
● Data Source:
BioConductor
● Keywords:
● Alias: distance2Genes
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genesWithPeaks
(Package: CSAR) :
Provide table of genes with read-enriched regions, and their location
Provide table of genes with read-enriched regions, and their location
● Data Source:
BioConductor
● Keywords:
● Alias: genesWithPeaks
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getPermutatedWinScores
(Package: CSAR) :
Obtain the read-enrichment score distribution under the null hypothesis
Obtain the read-enrichment score distribution under the null hypothesis
● Data Source:
BioConductor
● Keywords:
● Alias: getPermutatedWinScores
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getThreshold
(Package: CSAR) :
Calculate the threshold value corresponding to control FDR at a desired level
Calculate the threshold value corresponding to control FDR at a desired level
● Data Source:
BioConductor
● Keywords:
● Alias: getThreshold
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This function load the output file of a read mapping software (eg:SOAP)
● Data Source:
BioConductor
● Keywords:
● Alias: loadMappedReads
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mappedReads2Nhits
(Package: CSAR) :
Calculate number of overlapped extended reads per nucleotide position
Calculate number of overlapped extended reads per nucleotide position
● Data Source:
BioConductor
● Keywords:
● Alias: mappedReads2Nhits, mappedReads2Nhits_chr, pos2Nhits, pos2Nhits_old
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permutatedWinScores
(Package: CSAR) :
Calculate scores for permutated read-enriched regions
Calculate scores for permutated read-enriched regions
● Data Source:
BioConductor
● Keywords:
● Alias: permutatedWinScores
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score2wig
(Package: CSAR) :
Save the read-enrichment scores at each nucleotide position in a .wig file format
Save the read-enrichment scores at each nucleotide position in a .wig file format that can be visualize by a genome browser (eg: Integrated Genome Browser)
● Data Source:
BioConductor
● Keywords:
● Alias: LoadBinCSAR, score2wig
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