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MEDME.rnwusingutils::SweavePackage: 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:
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✨
DESCRIPTION
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:
- testMEDMEset - Dataset of class MEDMEset for testing MEDME
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
Last updated from:626920b489. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 263 | ||
| linux-devel-arm64 | WARNING | 300 | ||
| linux-devel-x86_64 | WARNING | 358 | ||
| source / vignettes | OK | 330 | ||
| linux-release-arm64 | WARNING | 311 | ||
| linux-release-x86_64 | WARNING | 354 | ||
| macos-release-arm64 | WARNING | 220 | ||
| macos-release-x86_64 | WARNING | 407 | ||
| macos-oldrel-arm64 | WARNING | 218 | ||
| macos-oldrel-x86_64 | WARNING | 324 | ||
| windows-devel | WARNING | 622 | ||
| windows-release | WARNING | 654 | ||
| windows-oldrel | WARNING | 631 | ||
| wasm-release | OK | 279 |
Exports:AMSCGCGcountchrinitializelogRMEDMEMEDME.predictMEDME.readFilesMEDME.writeFilesorgposRMSshowsmoothsmoothed
Dependencies:abindbackportsBiocGenericsBiostringsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11crayonDerivdoBydplyrdrcfarverforecastFormulafracdiffgenericsggplot2gluegtablegtoolsIRangesisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvminqamodelrmultcompmvtnormnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigplotrixpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangS4VectorsS7sandwichscalesSeqinfoSparseMstringistringrsurvivalTH.datatibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Determining the count of CpG dinucleotides for a set of genomic locations | CGcount |
| Determining the logistic model of MeDIP enrichment in respect to the expected DNA methylation level | MEDME |
| Applying the logistic model on MeDIP enrichment data | MEDME.predict |
| reading sgr or gff files for MEDME | MEDME.readFiles |
| writeFiles sgr or gff files from MEDME output | MEDME.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 data | smooth |
| Dataset of class MEDMEset for testing MEDME | testMEDMEset |