| 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 |