Licensing and citing | Introduction | The consensusSeekeR package | Loading consensusSeekeR package | Inputs | Positions and Ranges | Chromosomes information | Read NarrowPeak files | Case study: nucleosome positioning | Comparing nucleosome positioning results from different software | Case study: ChIP-Seq data | ChIP-Seq replicates from one experiment | ChIP-Seq data from multiple experiments | Parameters | Effect of the shrinkToFitPeakRegion parameter | Effect of the expandToFitPeakRegion parameter | Effect of the extendingSize parameter | Parallelizing consensusSeekeR | Acknowledgment | Session info | References
Package: consensusSeekeR 1.41.0
Astrid Deschênes
consensusSeekeR: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.
Authors:
consensusSeekeR_1.41.0.tar.gz
consensusSeekeR_1.41.0.zip(r-4.7)consensusSeekeR_1.41.0.zip(r-4.6)consensusSeekeR_1.41.0.zip(r-4.5)
consensusSeekeR_1.41.0.tgz(r-4.6-any)consensusSeekeR_1.41.0.tgz(r-4.5-any)
consensusSeekeR_1.41.0.tar.gz(r-4.7-any)consensusSeekeR_1.41.0.tar.gz(r-4.6-any)
consensusSeekeR_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
consensusSeekeR/json (API)
| # Install 'consensusSeekeR' in R: |
| install.packages('consensusSeekeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/adeschen/consensusseeker/issues
Datasets:
- A549_CTCF_MYJ_NarrowPeaks_partial - Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor
- A549_CTCF_MYJ_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor
- A549_CTCF_MYN_NarrowPeaks_partial - Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor
- A549_CTCF_MYN_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor
- A549_FOSL2_01_NarrowPeaks_partial - Genomic regions with the greatest evidence of transcription factor binding for the FOSL2 transcription factor
- A549_FOSL2_01_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor
- A549_FOXA1_01_NarrowPeaks_partial - Genomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor
- A549_FOXA1_01_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor
- A549_NR3C1_CFQ_NarrowPeaks_partial - Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
- A549_NR3C1_CFQ_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
- A549_NR3C1_CFR_NarrowPeaks_partial - Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
- A549_NR3C1_CFR_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
- A549_NR3C1_CFS_NarrowPeaks_partial - Ranges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
- A549_NR3C1_CFS_Peaks_partial - Sites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
- NOrMAL_nucleosome_positions - Nucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
- NOrMAL_nucleosome_ranges - Ranges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
- NucPosSimulator_nucleosome_positions - Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
- NucPosSimulator_nucleosome_ranges - Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
- PING_nucleosome_positions - Nucleosome positions detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
- PING_nucleosome_ranges - Ranges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
On BioConductor:consensusSeekeR-1.41.0(bioc 3.24)consensusSeekeR-1.40.0(bioc 3.23)
biologicalquestionchipseqgeneticsmultiplecomparisontranscriptionpeakdetectionsequencingcoveragechip-seq-analysisgenomic-data-analysisnucleosome-positioning
Last updated from:a6f0e12a31. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 209 | ||
| linux-devel-x86_64 | NOTE | 364 | ||
| source / vignettes | OK | 291 | ||
| linux-release-x86_64 | NOTE | 398 | ||
| macos-release-arm64 | NOTE | 330 | ||
| macos-oldrel-arm64 | NOTE | 170 | ||
| windows-devel | NOTE | 274 | ||
| windows-release | NOTE | 264 | ||
| windows-oldrel | NOTE | 260 | ||
| wasm-release | OK | 169 |
Exports:findConsensusPeakRegionsreadNarrowPeakFile
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsysvctrsXMLXVectoryaml
