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:

testMEDMEset - Dataset of class MEDMEset for testing MEDME

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.

microarray cpgisland dnamethylation

4.30 score 2 scripts 295 downloads 20 mentions 16 exports 86 dependencies

Last updated 2 months agofrom:0fb1eaddc1. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	WARNING	Nov 29 2024
R-4.5-linux-x86_64	WARNING	Nov 29 2024
R-4.4-win-x86_64	WARNING	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Nov 29 2024
R-4.4-mac-aarch64	WARNING	Nov 29 2024
R-4.3-win-x86_64	WARNING	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Nov 29 2024
R-4.3-mac-aarch64	WARNING	Nov 29 2024

Exports:AMS CG CGcount chr initialize logR MEDME MEDME.predict MEDME.readFiles MEDME.writeFiles org pos RMS show smooth smoothed

Dependencies:abind askpass backports BiocGenerics Biostrings boot broom car carData cli codetools colorspace cowplot cpp11 crayon curl Deriv doBy dplyr drc fansi farver Formula generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable gtools httr IRanges isoband jsonlite labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark mime minqa modelr multcomp munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plotrix purrr quantreg R6 RColorBrewer Rcpp RcppEigen rlang S4Vectors sandwich scales SparseM stringi stringr survival sys TH.data tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc zoo

MEDME

Rendered fromMEDME.rnwusingutils::Sweaveon Nov 29 2024.

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

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)