DMRcaller: Differentially Methylated Regions caller
Version 1.8.0

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

AuthorNicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk> and Jonathan Michael Foonlan Tsang <jmft2@cam.ac.uk>
Bioconductor views Coverage DNAMethylation DifferentialMethylation Sequencing Software
Date of publicationNone
MaintainerNicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk>
LicenseGPL-3
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")

Popular man pages

computeOverlapProfile: Compute Overlaps Profile
DMRcaller: Call Differentially Methylated Regions (DMRs) between two...
filterDMRs: Filter DMRs
plotMethylationProfileFromData: Plot methylation profile from data
poolMethylationDatasets: Pool methylation data
poolTwoMethylationDatasets: Pool two methylation datasets
readBismark: Read Bismark
See all...

All man pages Function index File listing

Man pages

analyseReadsInsideRegionsForCondition: Analyse reads inside regions for condition
computeDMRs: Compute DMRs
computeMethylationDataCoverage: Compute methylation data coverage
computeMethylationProfile: Compute methylation profile
computeOverlapProfile: Compute Overlaps Profile
DMRcaller: Call Differentially Methylated Regions (DMRs) between two...
DMRsNoiseFilterCG: The DMRs between WT and met1-3 in CG context
filterDMRs: Filter DMRs
GEs: The genetic elements data
getWholeChromosomes: Get whole chromosomes from methylation data
mergeDMRsIteratively: Merge DMRs iteratively
methylationDataList: The methylation data list
plotLocalMethylationProfile: Plot local methylation profile
plotMethylationDataCoverage: Plot methylation data coverage
plotMethylationProfile: Plot Methylation Profile
plotMethylationProfileFromData: Plot methylation profile from data
plotOverlapProfile: Plot overlap profile
poolMethylationDatasets: Pool methylation data
poolTwoMethylationDatasets: Pool two methylation datasets
readBismark: Read Bismark
readBismarkPool: Read Bismark pool
saveBismark: Save Bismark

Functions

DMRcaller Man page
DMRcaller-package Man page
DMRsNoiseFilterCG Man page
GEs Man page
analyseReadsInsideBins Source code
analyseReadsInsideBinsOneSample Source code
analyseReadsInsideRegions Source code
analyseReadsInsideRegionsForCondition Man page Source code Source code
analyseReadsInsideRegionsOneSample Source code
computeAdjuestedPValues Source code
computeDMRs Man page Source code
computeDMRsBins Source code
computeDMRsNeighbourhood Source code
computeDMRsNoiseFilter Source code
computeMethylationDataCoverage Man page Source code
computeMethylationProfile Man page Source code
computeOverlapProfile Man page Source code
computeaAjustedPValuesInDMRs Source code
countCytosinesInside Source code
countMethylationDataCoverage Source code
countOverlaps Source code
countTotalNumberOfCytosines Source code
epanechnicovKernel Source code
filterDMRs Man page Source code
fisherTest Source code
fisherTestPValue Source code
gaussianKernel Source code
getLongestDMRs Source code
getSumInRange Source code
getWholeChromosomes Man page Source code
joinDMRs Source code
joinMethylationData Source code
measureOverlaps Source code
mergeDMRsIteratively Man page Source code Source code
mergeRegions Source code
methylationDataList Man page
movingAverage Source code
movingSum Source code
plotGeneticElements Source code
plotLocalMethylationProfile Man page Source code
plotMethylationDataCoverage Man page Source code
plotMethylationProfile Man page Source code
plotMethylationProfileFromData Man page Source code
plotOverlapProfile Man page Source code
poolMethylationDatasets Man page Source code
poolTwoMethylationDatasets Man page Source code
printGenomicRanges Source code
readBismark Man page Source code
readBismarkPool Man page Source code
sColor Source code
sInteger Source code
saveBismark Man page Source code
scoreTest Source code
smartMergeDMRs Source code
splitGRangesEqualy Source code
stopIfNotAll Source code
sumReadsM Source code Source code
sumReadsM1 Source code
sumReadsM2 Source code
sumReadsN Source code Source code
sumReadsN1 Source code
sumReadsN2 Source code
validateContext Source code
validateGRanges Source code
validateMethylationData Source code
validateMethylationDataList Source code
validateMethylationProfile Source code
validateStatisticalTest Source code

Files

DESCRIPTION
NAMESPACE
R
R/DMRcaller.R
R/computeDMRs.R
R/coverage.R
R/generalFunctions.R
R/loadData.R
R/localProfile.R
R/movingAverage.R
R/profile.R
R/regions.R
R/statisticalTests.R
build
build/vignette.rds
data
data/DMRsNoiseFilterCG.RData
data/GEs.RData
data/datalist
data/methylationDataList.RData
inst
inst/NEWS
inst/doc
inst/doc/DMRcaller.R
inst/doc/DMRcaller.Rnw
inst/doc/DMRcaller.pdf
inst/unitTests
inst/unitTests/test_computeDMRs.R
man
man/DMRcaller.Rd
man/DMRsNoiseFilterCG.Rd
man/GEs.Rd
man/analyseReadsInsideRegionsForCondition.Rd
man/computeDMRs.Rd
man/computeMethylationDataCoverage.Rd
man/computeMethylationProfile.Rd
man/computeOverlapProfile.Rd
man/filterDMRs.Rd
man/getWholeChromosomes.Rd
man/mergeDMRsIteratively.Rd
man/methylationDataList.Rd
man/plotLocalMethylationProfile.Rd
man/plotMethylationDataCoverage.Rd
man/plotMethylationProfile.Rd
man/plotMethylationProfileFromData.Rd
man/plotOverlapProfile.Rd
man/poolMethylationDatasets.Rd
man/poolTwoMethylationDatasets.Rd
man/readBismark.Rd
man/readBismarkPool.Rd
man/saveBismark.Rd
tests
tests/runTests.R
vignettes
vignettes/DMRcaller.Rnw
vignettes/DMRcaller.bib
DMRcaller documentation built on May 20, 2017, 11 p.m.

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