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

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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.

Author
Astrid Deschenes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau [aut], Arnaud Droit [aut]
Date of publication
None
Maintainer
Astrid Louise Deschenes <Astrid-Louise.Deschenes@crchudequebec.ulaval.ca>
License
Artistic-2.0
Version
1.2.0
URLs

View on Bioconductor

Man pages

A549_CTCF_MYJ_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor...
A549_CTCF_MYJ_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_CTCF_MYN_NarrowPeaks_partial
Sites with the greatest evidence of transcription factor...
A549_CTCF_MYN_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_FOSL2_01_NarrowPeaks_partial
Genomic regions with the greatest evidence of transcription...
A549_FOSL2_01_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_FOXA1_01_NarrowPeaks_partial
Genomic regions with the greatest evidence of transcription...
A549_FOXA1_01_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_NR3C1_CFQ_NarrowPeaks_partial
Ranges with the greatest evidence of transcription factor...
A549_NR3C1_CFQ_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_NR3C1_CFR_NarrowPeaks_partial
Ranges with the greatest evidence of transcription factor...
A549_NR3C1_CFR_Peaks_partial
Sites with the greatest evidence of transcription factor...
A549_NR3C1_CFS_NarrowPeaks_partial
Ranges with the greatest evidence of transcription factor...
A549_NR3C1_CFS_Peaks_partial
Sites with the greatest evidence of transcription factor...
consensusSeekeR-package
consensusSeekeR: Detection of consensus peak regions inside a...
findConsensusPeakRegions
Extract regions sharing features in more than one experiment
findConsensusPeakRegionsForOneChrom
Extract regions sharing features in more than one experiment...
findConsensusPeakRegionsValidation
Parameter validation for the 'findConsensusPeakRegions'...
isInteger
Validate if a value is an integer
NOrMAL_nucleosome_positions
Nucleosome positions detected by the NOrMAL software using...
NOrMAL_nucleosome_ranges
Ranges associated to nucleosomes detected by the NOrMAL...
NucPosSimulator_nucleosome_positions
Nucleosome positions detected by the NucPosSimulator software...
NucPosSimulator_nucleosome_ranges
Ranges associated to nucleosomes detected by the...
PING_nucleosome_positions
Nucleosome positions detected by the PING software using...
PING_nucleosome_ranges
Ranges associated to nucleosomes detected by the PING...
readNarrowPeakFile
Extract narrow regions and peaks from a narrrowPeak file
refineRegion
Refine the selected region by using an iterative process.

Files in this package

consensusSeekeR/DESCRIPTION
consensusSeekeR/NAMESPACE
consensusSeekeR/NEWS
consensusSeekeR/R
consensusSeekeR/R/consensusSeekeR.R
consensusSeekeR/R/findConsensusPeakRegions.R
consensusSeekeR/R/findConsensusPeakRegionsIntern.R
consensusSeekeR/R/readNarrowPeak.R
consensusSeekeR/README.md
consensusSeekeR/build
consensusSeekeR/build/vignette.rds
consensusSeekeR/data
consensusSeekeR/data/A549_CTCF_MYJ_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_CTCF_MYJ_Peaks_partial.RData
consensusSeekeR/data/A549_CTCF_MYN_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_CTCF_MYN_Peaks_partial.RData
consensusSeekeR/data/A549_FOSL2_01_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_FOSL2_01_Peaks_partial.RData
consensusSeekeR/data/A549_FOXA1_01_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_FOXA1_01_Peaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFQ_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFQ_Peaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFR_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFR_Peaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFS_NarrowPeaks_partial.RData
consensusSeekeR/data/A549_NR3C1_CFS_Peaks_partial.RData
consensusSeekeR/data/NOrMAL_nucleosome_positions.RData
consensusSeekeR/data/NOrMAL_nucleosome_ranges.RData
consensusSeekeR/data/NucPosSimulator_nucleosome_positions.RData
consensusSeekeR/data/NucPosSimulator_nucleosome_ranges.RData
consensusSeekeR/data/PING_nucleosome_positions.RData
consensusSeekeR/data/PING_nucleosome_ranges.RData
consensusSeekeR/inst
consensusSeekeR/inst/CITATION
consensusSeekeR/inst/doc
consensusSeekeR/inst/doc/consensusSeekeR.R
consensusSeekeR/inst/doc/consensusSeekeR.Rmd
consensusSeekeR/inst/doc/consensusSeekeR.html
consensusSeekeR/inst/extdata
consensusSeekeR/inst/extdata/A549_FOSL2_ENCSR000BQO_MZW_part_chr_1_and_12.narrowPeak
consensusSeekeR/inst/extdata/Hosa_A549_FOSL2_ENCSR000BQO_MZT_peaks_part_chr1_and_12.narrowPeak
consensusSeekeR/inst/extdata/Hosa_A549_FOSL2_ENCSR000BQO_MZW_peaks_part_chr1_and_12.narrowPeak
consensusSeekeR/inst/unitTests
consensusSeekeR/inst/unitTests/Makefile.R
consensusSeekeR/inst/unitTests/test_findConsensusPeakRegions.R
consensusSeekeR/inst/unitTests/test_findConsensusPeakRegionsIntern.R
consensusSeekeR/inst/unitTests/test_readNarrowPeak.R
consensusSeekeR/man
consensusSeekeR/man/A549_CTCF_MYJ_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_CTCF_MYJ_Peaks_partial.Rd
consensusSeekeR/man/A549_CTCF_MYN_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_CTCF_MYN_Peaks_partial.Rd
consensusSeekeR/man/A549_FOSL2_01_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_FOSL2_01_Peaks_partial.Rd
consensusSeekeR/man/A549_FOXA1_01_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_FOXA1_01_Peaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFQ_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFQ_Peaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFR_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFR_Peaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFS_NarrowPeaks_partial.Rd
consensusSeekeR/man/A549_NR3C1_CFS_Peaks_partial.Rd
consensusSeekeR/man/NOrMAL_nucleosome_positions.Rd
consensusSeekeR/man/NOrMAL_nucleosome_ranges.Rd
consensusSeekeR/man/NucPosSimulator_nucleosome_positions.Rd
consensusSeekeR/man/NucPosSimulator_nucleosome_ranges.Rd
consensusSeekeR/man/PING_nucleosome_positions.Rd
consensusSeekeR/man/PING_nucleosome_ranges.Rd
consensusSeekeR/man/consensusSeekeR-package.Rd
consensusSeekeR/man/findConsensusPeakRegions.Rd
consensusSeekeR/man/findConsensusPeakRegionsForOneChrom.Rd
consensusSeekeR/man/findConsensusPeakRegionsValidation.Rd
consensusSeekeR/man/isInteger.Rd
consensusSeekeR/man/readNarrowPeakFile.Rd
consensusSeekeR/man/refineRegion.Rd
consensusSeekeR/tests
consensusSeekeR/tests/runTests.R
consensusSeekeR/vignettes
consensusSeekeR/vignettes/consensusSeekeR.Rmd
consensusSeekeR/vignettes/consensusSeekeR.bibtex
consensusSeekeR/vignettes/figures
consensusSeekeR/vignettes/figures/NR3C1_consensus.jpg
consensusSeekeR/vignettes/figures/ctcf_consensus.jpg
consensusSeekeR/vignettes/figures/extendNew.jpg
consensusSeekeR/vignettes/figures/nucleosomes.jpg
consensusSeekeR/vignettes/figures/peak_and_region.jpg
consensusSeekeR/vignettes/figures/shrink.jpg
consensusSeekeR/vignettes/figures/sizeEffect.jpg