DMRcaller: Differentially Methylated Regions caller

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>
Date of publicationNone
MaintainerNicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk>
LicenseGPL-3
Version1.6.0

View on Bioconductor

Functions

analyseReadsInsideRegionsForCondition Man page
computeDMRs Man page
computeMethylationDataCoverage Man page
computeMethylationProfile Man page
computeOverlapProfile Man page
DMRcaller Man page
DMRcaller-package Man page
DMRsNoiseFilterCG Man page
filterDMRs Man page
GEs Man page
getWholeChromosomes Man page
mergeDMRsIteratively Man page
methylationDataList Man page
plotLocalMethylationProfile Man page
plotMethylationDataCoverage Man page
plotMethylationProfile Man page
plotMethylationProfileFromData Man page
plotOverlapProfile Man page
poolMethylationDatasets Man page
poolTwoMethylationDatasets Man page
readBismark Man page
readBismarkPool Man page
saveBismark Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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