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)MEAL_1.43.0.zip(r-4.6)MEAL_1.43.0.zip(r-4.5)
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.

dnamethylationmicroarraysoftwarewholegenome

5.16 score 36 scripts 12 mentions 18 exports 220 dependencies

Last updated from:438858e149. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR1536
linux-devel-x86_64WARNING1747
source / vignettesOK1766
linux-release-x86_64WARNING1884
macos-release-arm64WARNING843
macos-oldrel-arm64WARNING1035
windows-develWARNING1167
windows-releaseWARNING1212
windows-oldrelWARNING1427
wasm-releaseOK1407

Exports:correlationMethExprsexportResultsfilterResultsgetGeneValsgetProbeResultsgetRDAresultsplotFeatureplotRDAplotRegionrunBlockFinderrunBumphunterrunDiffMeanAnalysisrunDiffVarAnalysisrunDMRcaterunPipelinerunRDArunRegionAnalysistopRDAhits

Dependencies:abindannotateAnnotationDbiAnnotationFilteraskpassbackportsbase64base64encbeanplotBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibbumphuntercachemcalibratecheckmatecigarilloclicliprclueclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirdichromatdigestdir.expirydoRNGdplyredgeRensembldbevaluatefarverfastICAfastmapFDb.InfiniumMethylation.hg19filelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2ggrepelglueGO.dbgridExtragtableGvizh5mreadHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaiointerpIRangesisobandisvaiteratorsJADEjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimissMethylMultiDataSetmulttestnlmennetnor1mixopensslorg.Hs.eg.dbpermutepillarpkgconfigplyrpngpreprocessCoreprettyunitsprogressProtGenericspurrrqqmanquadprogqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSpectraRSQLiterstudioapirtracklayerruvrvestS4ArraysS4VectorsS7sassscalesscrimeselectrSeqinfosiggenesSmartSVAsnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttinytexTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8VariantAnnotationvctrsveganviridisLitevroomwithrxfunXMLxml2xtableXVectoryaml

Expression and Methylation Analysis with MEAL
Introduction | Methylation Analysis | Running the analyses | Expression Analysis | Running the analysis | Methylation and gene expression integration | Conclusions | References
Rendered fromcaseExample.Rmdusingknitr::rmarkdown

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

Methylation Analysis with MEAL
Introduction | Input data | Analyzing Methylation data | Pipeline | Managing the results | Plotting the results | Manhattan plot | Volcano plot | QQplot | Features | Regional plotting | Methods wrappers | Differences of mean analysis | Differences of Variance analysis | RDA | Managing and plotting RDA results | Session Info | References
Rendered fromMEAL.Rmdusingknitr::rmarkdown

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