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consensusSeekeR : Detection of consensus regions inside a group of experiments using genomic positions and genomic ranges

This R package compares multiple narrowPeak data from different experiments to extract common peak regions. The size of the analyzed region is adjustable, as well as the number of experiences in which a peak must be present to tag a potential region as a consensus region. If needed, the consensus regions can be extended to cover the entire regions of enclosed peaks.

Authors

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

See Arnaud Droit Lab website.

Bioconductor Package

consensusSeekeR is now an official package of Bioconductor. The current development release can be directly downloaded from their website: Current devel release

Maintainer

Astrid Deschênes

License

This package and the underlying consensusSeekeR code are distributed under the Artistic license 2.0. You are free to use and redistribute this software.

For more information on Artistic 2.0 License see http://opensource.org/licenses/Artistic-2.0

Bugs/Feature requests

If you have any bugs or feature requests, let us know. Thanks!

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Version

Version

1.0.2

License

Artistic-2.0

Issues

1

Pull Requests

0

Stars

3

Forks

3

Maintainer

Astrid Deschenes

Last Published

February 15th, 2017

Functions in consensusSeekeR (1.0.2)

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_FOXA1_01_Peaks_partial

Sites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
NOrMAL_nucleosome_positions

Nucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. 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.
readNarrowPeakFile

Extract narrow regions and peaks from a narrrowPeak file
A549_FOXA1_01_NarrowPeaks_partial

Genomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
A549_CTCF_MYN_Peaks_partial

Sites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
A549_FOSL2_01_NarrowPeaks_partial

Genomic regions with the greatest evidence of transcription factor binding for the FOSL2 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)
NOrMAL_nucleosome_ranges

Ranges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
A549_FOSL2_01_Peaks_partial

Sites with the greatest evidence of transcription factor binding for the FOSL2 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_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.
isInteger

Validate if a value is an integer
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_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.
PING_nucleosome_positions

Nucleosome positions detected by the PING 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.
consensusSeekeR-package

consensusSeekeR: Detection of consensus peak regions inside a group of experiments using narrowPeak files
refineRegion

Refine the selected region by using an iterative process.
PING_nucleosome_ranges

Ranges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. 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_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.
findConsensusPeakRegionsForOneChrom

Extract regions sharing features in more than one experiment for one specific chromosome.
NucPosSimulator_nucleosome_positions

Nucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
findConsensusPeakRegions

Extract regions sharing features in more than one experiment
findConsensusPeakRegionsValidation

Parameter validation for the findConsensusPeakRegions function