Package: recountmethylation 1.15.0

Sean K Maden

recountmethylation: Access and analyze public DNA methylation array data compilations

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

Authors:Sean K Maden [cre, aut], Brian Walsh [aut], Kyle Ellrott [aut], Kasper D Hansen [aut], Reid F Thompson [aut], Abhinav Nellore [aut]

recountmethylation_1.15.0.tar.gz
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recountmethylation.pdf |recountmethylation.html✨
recountmethylation/json (API)
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Bug tracker:https://github.com/metamaden/recountmethylation/issues

On BioConductor:recountmethylation-1.15.0(bioc 3.20)recountmethylation-1.14.0(bioc 3.19)

bioconductor-package

21 exports 0.82 score 141 dependencies

Last updated 2 months agofrom:c0294315dd

Exports:bactrlbathreshdata_mdpostgds_idat2rggds_idatqueryget_crossreactive_cpgsget_qcsignalget_rmdlget_servermatrixgetdb_h5_rggetdb_h5_testgetdb_h5se_gmgetdb_h5se_grgetdb_h5se_rggetdb_h5se_testgetrghreadmatchds_1to2rgseservermatrixsmfilt

Dependencies:abindannotateAnnotationDbiaskpassbase64basiliskbasilisk.utilsbeanplotBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoRNGdplyrfansifastmapfilelockforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueHDF5ArrayherehmshttrilluminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLRCurlreadrreshaperestfulrreticulaterhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsrprojrootRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscrimesiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectoryamlzlibbioc