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

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

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

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