Package: CSAR 1.59.0
Jose M Muino
CSAR: Statistical tools for the analysis of ChIP-seq data
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.
Authors:
CSAR_1.59.0.tar.gz
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CSAR.pdf |CSAR.html✨
CSAR/json (API)
| # Install 'CSAR' in R: |
| install.packages('CSAR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- TAIR8_genes_test - Partial dataset of a ChIP-seq experiment
- controlSEP3_test - Partial dataset of a ChIP-seq experiment
- sampleSEP3_test - Partial dataset of a ChIP-seq experiment
On BioConductor:CSAR-1.57.0(bioc 3.20)CSAR-1.56.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:43ca1bcff3. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 30 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 30 2024 |
| R-4.3-win-x86_64 | NOTE | Oct 30 2024 |
| R-4.3-mac-x86_64 | NOTE | Oct 30 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 30 2024 |
Exports:ChIPseqScoredistance2GenesgenesWithPeaksgetPermutatedWinScoresgetThresholdLoadBinCSARloadMappedReadsmappedReads2NhitsmappedReads2Nhits_chrpermutatedWinScorespos2Nhitsscore_chrscore2wigsigWinsigWin_chr
Dependencies:askpassBiocGenericscurlGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Statistical tools for the analysis of ChIP-seq data | CSAR-package |
| Calculate read-enrichment scores for each nucleotide position | ChIPseqScore score_chr |
| Calculate relative positions of read-enriched regions regarding gene position | distance2Genes |
| Provide table of genes with read-enriched regions, and their location | genesWithPeaks |
| Obtain the read-enrichment score distribution under the null hypothesis | getPermutatedWinScores |
| Calculate the threshold value corresponding to control FDR at a desired level | getThreshold |
| Load mapped reads | loadMappedReads |
| Calculate number of overlapped extended reads per nucleotide position | mappedReads2Nhits mappedReads2Nhits_chr pos2Nhits pos2Nhits_old |
| Calculate scores for permutated read-enriched regions | permutatedWinScores |
| Partial dataset of a ChIP-seq experiment | controlSEP3_test sampleSEP3_test TAIR8_genes_test |
| Save the read-enrichment scores at each nucleotide position in a .wig file format | LoadBinCSAR score2wig |
| Calculate regions of read-enrichment | sigWin sigWin_chr |