Package: MEDME 1.73.0

Mattia Pelizzola

MEDME: Modelling Experimental Data from MeDIP Enrichment

MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments

Authors:Mattia Pelizzola and Annette Molinaro

MEDME_1.73.0.tar.gz
MEDME_1.73.0.zip(r-4.7)MEDME_1.73.0.zip(r-4.6)MEDME_1.73.0.zip(r-4.5)
MEDME_1.73.0.tgz(r-4.6-x86_64)MEDME_1.73.0.tgz(r-4.6-arm64)MEDME_1.73.0.tgz(r-4.5-x86_64)MEDME_1.73.0.tgz(r-4.5-arm64)
MEDME_1.73.0.tar.gz(r-4.7-arm64)MEDME_1.73.0.tar.gz(r-4.7-x86_64)MEDME_1.73.0.tar.gz(r-4.6-arm64)MEDME_1.73.0.tar.gz(r-4.6-x86_64)
MEDME_1.73.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MEDME/json (API)

# Install 'MEDME' in R:
install.packages('MEDME', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:MEDME-1.73.0(bioc 3.24)MEDME-1.72.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarraycpgislanddnamethylation

4.30 score 2 scripts 430 downloads 20 mentions 16 exports 84 dependencies

Last updated from:626920b489. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR272
linux-devel-arm64WARNING302
linux-devel-x86_64WARNING424
source / vignettesOK365
linux-release-arm64WARNING300
linux-release-x86_64WARNING348
macos-release-arm64WARNING234
macos-release-x86_64WARNING665
macos-oldrel-arm64WARNING208
macos-oldrel-x86_64WARNING573
windows-develWARNING704
windows-releaseWARNING670
windows-oldrelWARNING657
wasm-releaseOK257

Exports:AMSCGCGcountchrinitializelogRMEDMEMEDME.predictMEDME.readFilesMEDME.writeFilesorgposRMSshowsmoothsmoothed

Dependencies:abindbackportsBiocGenericsBiostringsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11crayonDerivdoBydplyrdrcfarverforecastFormulafracdiffgenericsggplot2gluegtablegtoolsIRangesisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplotrixpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS4VectorsS7sandwichscalesSeqinfoSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXVectorzoo

MEDME

Rendered fromMEDME.rnwusingutils::Sweaveon May 30 2026.

Last update: 2013-11-01
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Determining the count of CpG dinucleotides for a set of genomic locationsCGcount
Determining the logistic model of MeDIP enrichment in respect to the expected DNA methylation levelMEDME
Applying the logistic model on MeDIP enrichment dataMEDME.predict
reading sgr or gff files for MEDMEMEDME.readFiles
writeFiles sgr or gff files from MEDME outputMEDME.writeFiles
Class "MEDMEset"AMS AMS,MEDMEset-method CG CG,MEDMEset-method CGcounts chr chr,MEDMEset-method initialize,MEDMEset-method logR logR,MEDMEset-method MEDMEset-class org org,MEDMEset-method organism pos pos,MEDMEset-method RMS RMS,MEDMEset-method show,MEDMEset-method smoothed smoothed,MEDMEset-method [,MEDMEset-method
Determining weighted MeDIP datasmooth
Dataset of class MEDMEset for testing MEDMEtestMEDMEset