Package: consensusSeekeR 1.35.0

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:Astrid Deschênes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau [aut], Arnaud Droit [aut]

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consensusSeekeR.pdf |consensusSeekeR.html✨
consensusSeekeR/json (API)
NEWS

# Install 'consensusSeekeR' in R:
install.packages('consensusSeekeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.35.0(bioc 3.21)consensusSeekeR-1.34.0(bioc 3.20)

biologicalquestionchipseqgeneticsmultiplecomparisontranscriptionpeakdetectionsequencingcoveragechip-seq-analysisgenomic-data-analysisnucleosome-positioning

5.43 score 1 stars 1 packages 5 scripts 220 downloads 2 exports 58 dependencies

Last updated 2 months agofrom:937d3ad47a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-winNOTEDec 07 2024
R-4.5-linuxNOTEDec 07 2024
R-4.4-winNOTEDec 07 2024
R-4.4-macNOTEDec 07 2024
R-4.3-winNOTEDec 07 2024
R-4.3-macNOTEDec 07 2024

Exports:findConsensusPeakRegionsreadNarrowPeakFile

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc

Detection of consensus regions inside a group of experiments

Astrid Deschênes, Fabien Claude Lamaze, Pascal Belleau and Arnaud Droit

Rendered fromconsensusSeekeR.Rmdusingknitr::rmarkdownon Dec 07 2024.

Last update: 2024-02-22
Started: 2015-11-13

Readme and manuals

Help Manual

Help pageTopics
consensusSeekeR: Detection of consensus peak regions inside a group of experiments using narrowPeak filesconsensusSeekeR-package consensusSeekeR
Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)A549_CTCF_MYJ_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)A549_CTCF_MYJ_Peaks_partial
Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)A549_CTCF_MYN_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)A549_CTCF_MYN_Peaks_partial
Genomic regions with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)A549_FOSL2_01_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)A549_FOSL2_01_Peaks_partial
Genomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)A549_FOXA1_01_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)A549_FOXA1_01_Peaks_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_NarrowPeaks_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_CFQ_Peaks_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_NarrowPeaks_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_CFR_Peaks_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_NarrowPeaks_partial
Sites 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
Extract regions sharing features in more than one experimentfindConsensusPeakRegions
Nucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.NOrMAL_nucleosome_positions
Ranges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.NOrMAL_nucleosome_ranges
Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.NucPosSimulator_nucleosome_positions
Ranges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.NucPosSimulator_nucleosome_ranges
Nucleosome positions detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.PING_nucleosome_positions
Ranges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.PING_nucleosome_ranges
Extract narrow regions and peaks from a narrrowPeak filereadNarrowPeakFile