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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("consensusSeekeR")
AuthorAstrid Deschenes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau [aut], Arnaud Droit [aut]
Bioconductor views BiologicalQuestion ChIPSeq Coverage Genetics MultipleComparison PeakDetection Sequencing Transcription
Date of publicationNone
MaintainerAstrid Deschenes <adeschen@hotmail.com>
LicenseArtistic-2.0
Version1.4.0
https://github.com/ArnaudDroitLab/consensusSeekeR

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.

Functions

A549_CTCF_MYJ_NarrowPeaks_partial Man page
A549_CTCF_MYJ_Peaks_partial Man page
A549_CTCF_MYN_NarrowPeaks_partial Man page
A549_CTCF_MYN_Peaks_partial Man page
A549_FOSL2_01_NarrowPeaks_partial Man page
A549_FOSL2_01_Peaks_partial Man page
A549_FOXA1_01_NarrowPeaks_partial Man page
A549_FOXA1_01_Peaks_partial Man page
A549_NR3C1_CFQ_NarrowPeaks_partial Man page
A549_NR3C1_CFQ_Peaks_partial Man page
A549_NR3C1_CFR_NarrowPeaks_partial Man page
A549_NR3C1_CFR_Peaks_partial Man page
A549_NR3C1_CFS_NarrowPeaks_partial Man page
A549_NR3C1_CFS_Peaks_partial Man page
consensusSeekeR Man page
consensusSeekeR-package Man page
findConsensusPeakRegions Man page
findConsensusPeakRegionsForOneChrom Man page
findConsensusPeakRegionsValidation Man page
isInteger Man page
NOrMAL_nucleosome_positions Man page
NOrMAL_nucleosome_ranges Man page
NucPosSimulator_nucleosome_positions Man page
NucPosSimulator_nucleosome_ranges Man page
PING_nucleosome_positions Man page
PING_nucleosome_ranges Man page
readNarrowPeakFile Man page
refineRegion Man page

Files

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