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'))

Peer review:

Datasets:

On BioConductor:MEDME-1.65.0(bioc 3.20)MEDME-1.64.0(bioc 3.19)

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 268 downloads 20 mentions 16 exports 86 dependencies

Last updated 23 days agofrom:0fb1eaddc1. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64WARNINGOct 31 2024
R-4.5-linux-x86_64WARNINGOct 30 2024
R-4.4-win-x86_64WARNINGOct 31 2024
R-4.4-mac-x86_64WARNINGOct 31 2024
R-4.4-mac-aarch64WARNINGOct 31 2024
R-4.3-win-x86_64WARNINGOct 31 2024
R-4.3-mac-x86_64WARNINGOct 31 2024
R-4.3-mac-aarch64WARNINGOct 31 2024

Exports:AMSCGCGcountchrinitializelogRMEDMEMEDME.predictMEDME.readFilesMEDME.writeFilesorgposRMSshowsmoothsmoothed

Dependencies:abindaskpassbackportsBiocGenericsBiostringsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11crayoncurlDerivdoBydplyrdrcfansifarverFormulagenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablegtoolshttrIRangesisobandjsonlitelabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqamodelrmultcompmunsellmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotrixpurrrquantregR6RColorBrewerRcppRcppEigenrlangS4VectorssandwichscalesSparseMstringistringrsurvivalsysTH.datatibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioczoo

MEDME

Rendered fromMEDME.rnwusingutils::Sweaveon Oct 30 2024.

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