Package: MEDME 1.67.0

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

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MEDME.pdf |MEDME.html✨
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-1.67.0(bioc 3.21)MEDME-1.66.0(bioc 3.20)

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 378 downloads 20 mentions 16 exports 88 dependencies

Last updated 5 months agofrom:0fb1eaddc1. Checks:1 OK, 11 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-win-x86_64WARNINGMar 29 2025
R-4.5-mac-x86_64WARNINGMar 29 2025
R-4.5-mac-aarch64WARNINGMar 29 2025
R-4.5-linux-x86_64WARNINGMar 29 2025
R-4.4-win-x86_64WARNINGMar 29 2025
R-4.4-mac-x86_64WARNINGMar 29 2025
R-4.4-mac-aarch64WARNINGMar 29 2025
R-4.4-linux-x86_64WARNINGMar 29 2025
R-4.3-win-x86_64WARNINGMar 29 2025
R-4.3-mac-x86_64WARNINGMar 29 2025
R-4.3-mac-aarch64WARNINGMar 29 2025

Exports:AMSCGCGcountchrinitializelogRMEDMEMEDME.predictMEDME.readFilesMEDME.writeFilesorgposRMSshowsmoothsmoothed

Dependencies:abindaskpassbackportsBiocGenericsBiostringsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11crayoncurlDerivdoBydplyrdrcfansifarverFormulagenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablegtoolshttrIRangesisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotrixpurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackreformulasrlangS4VectorssandwichscalesSparseMstringistringrsurvivalsysTH.datatibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzoo

MEDME

Rendered fromMEDME.rnwusingutils::Sweaveon Mar 29 2025.

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