Package: methodical 1.1.0

Richard Heery

methodical: Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Authors:Richard Heery [aut, cre]

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On BioConductor:methodical-1.1.0(bioc 3.20)methodical-1.0.0(bioc 3.19)

bioconductor-package

26 exports 1.69 score 115 dependencies

Last updated 2 months agofrom:3aab960ef1

Exports:annotateGRangesannotatePlotcalculateMethSiteTranscriptCorscalculateRegionMethylationTranscriptCorscalculateSmoothedMethodicalScorescreateRandomRegionsextractGRangesMethSiteValuesextractMethSitesFromGenomefindTMRskallistoIndexkallistoQuantifyliftoverMethRSEmakeMethRSEFromArrayFilesmakeMethRSEFromBedgraphsmaskRangesInRSEmethrixToRSEplotMethodicalScoresplotMethSiteCorCoefsplotMethylationValuesplotTMRsrangesRelativeToTSSrapidCorTestsampleMethSitesstrandedDistancesummarizeRegionMethylationsumTranscriptValuesForGenes

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrExperimentHubfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtableHDF5ArrayhttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppRollRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc