CSAR-package |
Statistical tools for the analysis of ChIP-seq data |
ChIPseqScore |
Calculate read-enrichment scores for each nucleotide position |
controlSEP3_test |
Partial dataset of a ChIP-seq experiment |
distance2Genes |
Calculate relative positions of read-enriched regions regarding gene position |
genesWithPeaks |
Provide table of genes with read-enriched regions, and their location |
getPermutatedWinScores |
Obtain the read-enrichment score distribution under the null hypothesis |
getThreshold |
Calculate the threshold value corresponding to control FDR at a desired level |
LoadBinCSAR |
Save the read-enrichment scores at each nucleotide position in a .wig file format |
loadMappedReads |
Load mapped reads |
mappedReads2Nhits |
Calculate number of overlapped extended reads per nucleotide position |
mappedReads2Nhits_chr |
Calculate number of overlapped extended reads per nucleotide position |
permutatedWinScores |
Calculate scores for permutated read-enriched regions |
pos2Nhits |
Calculate number of overlapped extended reads per nucleotide position |
pos2Nhits_old |
Calculate number of overlapped extended reads per nucleotide position |
sampleSEP3_test |
Partial dataset of a ChIP-seq experiment |
score2wig |
Save the read-enrichment scores at each nucleotide position in a .wig file format |
score_chr |
Calculate read-enrichment scores for each nucleotide position |
sigWin |
Calculate regions of read-enrichment |
sigWin_chr |
Calculate regions of read-enrichment |
TAIR8_genes_test |
Partial dataset of a ChIP-seq experiment |