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

Functions

CpGsDemo Man page
determineGroupComps Man page
findComps Man page
M3D Man page
M3D-package Man page
M3D_Para Man page
M3D_Para_lite Man page
M3D_Single Man page
M3D_Wrapper Man page
M3D_Wrapper_lite Man page
median_freq Man page
medianFreq Man page
MMDlistDemo Man page
PDemo Man page
plotCoverageSampleProfiles Man page
plotMethProfile Man page
plotMethSampleProfiles Man page
pvals Man page
pvals_lite Man page
readBedFiles Man page
readBedRaw Man page
rrbsDemo Man page
test_colData_structure Man page

Files

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

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

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