Package: methylclock 1.13.0

Dolors Pelegri-Siso

methylclock: Methylclock - DNA methylation-based clocks

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Authors:Dolors Pelegri-Siso [aut, cre], Juan R. Gonzalez [aut]

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methylclock.pdf |methylclock.html
methylclock/json (API)
NEWS

# Install 'methylclock' in R:
install.packages('methylclock', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/isglobal-brge/methylclock/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:methylclock-1.11.0(bioc 3.20)methylclock-1.10.0(bioc 3.19)

dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalization

6.43 score 39 stars 23 scripts 318 downloads 12 exports 288 dependencies

Last updated 23 days agofrom:5639edc30c. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:checkClockscheckClocksGAcommonClockCpgsDNAmAgeDNAmGAgetCellTypeReferenceload_DNAm_Clocks_dataload_DNAmGA_Clocks_datameffilEstimateCellCountsFromBetasmeffilListCellTypeReferencesplotCorClocksplotDNAmAge

Dependencies:abindannotateAnnotationDbiAnnotationForgeAnnotationHubAnnotationHubDataaskpassbackportsbase64base64encbeanplotBHBiobaseBiocBaseUtilsBiocCheckBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiocViewsbiomaRtBiostringsbitbit64bitopsblobbootbrewbriobroombslibbumphuntercachemcallrcarcarDatacellrangerclicliprclustercodetoolscolorspacecommonmarkconfintrconflictedcorrplotcowplotcpp11crayoncredentialscurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsDerivdescdevtoolsdiffobjdigestdoBydoRNGdownlitdplyrdtplyrdynamicTreeCutellipsisevaluateExperimentHubExperimentHubDatafansifarverfastmapfilelockfontawesomeforcatsforeachformatRFormulafsfutile.loggerfutile.optionsgarglegenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOquerygertggplot2ggpmiscggppggpubrggrepelggsciggsignifghgitcredsgluegoogledrivegooglesheets4graphgridExtragtablehavenHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2idsilluminaioimputeiniIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelifecyclelimmalme4lmodel2locfitlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustmemoisemethylclockDatamgcvmicrobenchmarkmimeminfiminiUIminqamodelrmultcompmultcompViewmulttestmunsellmvtnormnlmenloptrnnetnor1mixnumDerivopensslOrganismDbipbkrtestPerformanceAnalyticspillarpkgbuildpkgconfigpkgdownpkgloadplanetplogrplyrpngpolynompraisepreprocessCoreprettyunitsprocessxprofvisprogresspromisespspurrrquadprogquantregR.methodsS3R.ooR.utilsR6raggrappdirsRBGLrcmdcheckRColorBrewerRcppRcppEigenRCurlreadrreadxlrematchrematch2remotesrentrezreprexreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsroxygen2RPMMrprojrootRsamtoolsRSQLiterstatixrstudioapirtracklayerRUnitrversionsrvestS4ArraysS4VectorssandwichsassscalesscrimeselectrsessioninfoshinysiggenessnowsourcetoolsSparseArraySparseMsparseMatrixStatssplus2RstatmodstringdiststringistringrSummarizedExperimentsurvivalsyssystemfontstestthattextshapingTH.datatibbletidyrtidyselecttidyversetimechangetinytextxdbmakertzdbUCSC.utilsurlcheckerusethisutf8uuidvctrsviridisLitevroomwaldowhiskerwithrxfunXMLxml2xopenxtablextsXVectoryamlzipzlibbioczoo

Chronological and gestational DNAm age estimation using different methylation-based clocks

Rendered frommethylclock.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-07-11
Started: 2019-03-15