Package: MEAL 1.43.0

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_1.43.0.tar.gz
MEAL_1.43.0.zip(r-4.7-any)MEAL_1.43.0.zip(r-4.6-any)MEAL_1.43.0.zip(r-4.5-any)
MEAL_1.43.0.tgz(r-4.6-any)MEAL_1.43.0.tgz(r-4.5-any)
MEAL_1.43.0.tar.gz(r-4.7-any)MEAL_1.43.0.tar.gz(r-4.6-any)
MEAL_1.43.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MEAL/json (API)

# Install 'MEAL' in R:

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

On BioConductor:MEAL-1.43.0(bioc 3.24)MEAL-1.42.0(bioc 3.23)

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

dnamethylation microarray software wholegenome

4.01 score 51 scripts 669 downloads 12 mentions 18 exports 218 dependencies

Last updated from:438858e149. Checks:9 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	1201
linux-devel	ERROR	1264
source / vignettes	ERROR	2651
linux-release	ERROR	1796
macos-release	ERROR	1163
macos-oldrel	ERROR	1113
windows-devel	ERROR	1077
windows-release	ERROR	1222
windows-oldrel	ERROR	1225
wasm-release	OK	1324

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 BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bumphunter cachem calibrate checkmate cigarillo cli clipr clue cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dichromat digest dir.expiry doRNG dplyr edgeR ensembldb evaluate farver fastICA fastmap FDb.InfiniumMethylation.hg19 filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 ggrepel glue GO.db gridExtra gtable Gviz h5mread 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 nlme nnet nor1mix openssl org.Hs.eg.db permute pillar pkgconfig plyr png preprocessCore prettyunits progress ProtGenerics purrr qqman quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSpectra RSQLite rstudioapi rtracklayer ruv S4Arrays S4Vectors S7 sass scales scrime Seqinfo 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 viridisLite vroom withr xfun XML xml2 xtable XVector yaml

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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

Package: MEAL 1.43.0

MEAL: Perform methylation analysis

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