Package: MEAL 1.35.0

Xavier Escribà Montagut

MEAL: Perform methylation analysis

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

Authors:Carlos Ruiz-Arenas [aut, cre], Juan R. Gonzalez [aut]

MEAL_1.35.0.tar.gz
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MEAL.pdf |MEAL.html✨
MEAL/json (API)
NEWS

# Install 'MEAL' in R:

install.packages('MEAL', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:MEAL-1.35.0(bioc 3.20)MEAL-1.34.0(bioc 3.19)

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

bioconductor-package

18 exports 2.80 score 216 dependencies 12 mentions

Last updated 2 months agofrom:16f66a8e01

Exports:correlationMethExprs exportResults filterResults getGeneVals getProbeResults getRDAresults plotFeature plotRDA plotRegion runBlockFinder runBumphunter runDiffMeanAnalysis runDiffVarAnalysis runDMRcate runPipeline runRDA runRegionAnalysis topRDAhits

Dependencies:abind annotate AnnotationDbi AnnotationFilter askpass backports base64 base64enc beanplot BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bumphunter cachem calibrate checkmate cli clipr clue cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dichromat digest doRNG dplyr edgeR ensembldb evaluate fansi farver fastICA fastmap FDb.InfiniumMethylation.hg19 filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 ggrepel glue GO.db gridExtra gtable Gviz HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio interp IRanges isoband isva iterators JADE jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi missMethyl MultiDataSet multtest munsell nlme nnet nor1mix openssl org.Hs.eg.db permute pillar pkgconfig plogr plyr png preprocessCore prettyunits progress ProtGenerics purrr qqman quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSpectra RSQLite rstudioapi rtracklayer ruv S4Arrays S4Vectors sass scales scrime siggenes SmartSVA snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sva sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 VariantAnnotation vctrs vegan viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

Expression and Methylation Analysis with MEAL

Carlos Ruiz, Juan R. González

Rendered fromcaseExample.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2021-01-21
Started: 2017-09-12

Methylation Analysis with MEAL

Carlos Ruiz, Juan R. González

Rendered fromMEAL.Rmdusingknitr::rmarkdownon Jul 02 2024.

Last update: 2021-01-21
Started: 2017-09-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute signification of RDA test	computeRDAR2
Computes the correlation between methylation and expression	correlationMethExprs
Exports results data.frames to csv files.	exportResults
Filter the data.frame obtained from probe analysis	filterResults
Get all probes related to a gene	getGeneVals
Obtain probe results from a 'ResultSet'	getProbeResults
Get a summary of RDA results	getRDAresults
MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data	MEAL
Defunct functions	MEAL-defunct
Plot values of a feature	plotFeature
Plot RDA results	plotRDA
Plot results in a genomic region	plotRegion
Run blockFinder	runBlockFinder
Run bumphunter	runBumphunter
Run differential mean analysis	runDiffMeanAnalysis
Run differential variance analysis	runDiffVarAnalysis
Run DMRcate	runDMRcate
Perform differential methylation analysis	runPipeline
Calculate RDA for a set	runRDA
Run different DMR detection methods	runRegionAnalysis
Get the top features associated with the RDA	topRDAhits