M3D: Identifies differentially methylated regions across testing groups

This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.

AuthorTom Mayo
Date of publicationNone
MaintainerTom Mayo <t.mayo@ed.ac.uk>
LicenseArtistic License 2.0
Version1.8.0

View on Bioconductor

Files in this package

M3D/.BBSoptions
M3D/DESCRIPTION
M3D/NAMESPACE
M3D/NEWS
M3D/R
M3D/R/M3D.R M3D/R/M3D_Para.R M3D/R/M3D_Para_lite.R M3D/R/M3D_Single.R M3D/R/M3D_Wrapper.R M3D/R/M3D_Wrapper_lite.R M3D/R/RcppExports.R M3D/R/determineGroupComps.R M3D/R/findComps.R M3D/R/medianFreq.R M3D/R/plotCoverageSampleProfiles.R M3D/R/plotMethProfile.R M3D/R/plotMethSampleProfiles.R M3D/R/pvals.R M3D/R/pvals_lite.R M3D/R/readBedFiles.R M3D/R/readBedRaw.R M3D/R/test_colData_structure.R
M3D/build
M3D/build/vignette.rds
M3D/data
M3D/data/CpGsDemo.rda
M3D/data/MMDlistDemo.rda
M3D/data/PDemo.rda
M3D/data/datalist
M3D/data/rrbsDemo.rda
M3D/inst
M3D/inst/doc
M3D/inst/doc/M3D_vignette.R
M3D/inst/doc/M3D_vignette.Rnw
M3D/inst/doc/M3D_vignette.pdf
M3D/man
M3D/man/CpGsDemo.Rd M3D/man/M3D-package.Rd M3D/man/M3D_Para.Rd M3D/man/M3D_Para_lite.Rd M3D/man/M3D_Single.Rd M3D/man/M3D_Wrapper.Rd M3D/man/M3D_Wrapper_lite.Rd M3D/man/MMDlistDemo.Rd M3D/man/PDemo.Rd M3D/man/determineGroupComps.Rd M3D/man/findComps.Rd M3D/man/medianFreq.Rd M3D/man/median_freq.Rd M3D/man/plotCoverageSampleProfiles.Rd M3D/man/plotMethProfile.Rd M3D/man/plotMethSampleProfiles.Rd M3D/man/pvals.Rd M3D/man/pvals_lite.Rd M3D/man/readBedFiles.Rd M3D/man/readBedRaw.Rd M3D/man/rrbsDemo.Rd M3D/man/test_colData_structure.Rd
M3D/src
M3D/src/RcppExports.cpp
M3D/src/cpp_fns.cpp
M3D/tests
M3D/tests/testthat
M3D/tests/testthat.R
M3D/tests/testthat/test_hidden_fns.R
M3D/tests/testthat/test_lite_fns.R
M3D/tests/testthat/test_non_lite_fns.R
M3D/vignettes
M3D/vignettes/M3D_vignette-M3DhistPlot.pdf
M3D/vignettes/M3D_vignette-M3DstatPlot.pdf
M3D/vignettes/M3D_vignette.Rnw
M3D/vignettes/M3D_vignette.bib

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