DMRcaller: Differentially Methylated Regions caller

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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.

Author
Nicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk> and Jonathan Michael Foonlan Tsang <jmft2@cam.ac.uk>
Date of publication
None
Maintainer
Nicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk>
License
GPL-3
Version
1.6.0

View on Bioconductor

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

Files in this package

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