Package: scmeth 1.27.0

Divy Kangeyan

scmeth: Functions to conduct quality control analysis in methylation data

Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.

Authors:Divy Kangeyan <[email protected]>

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scmeth.pdf |scmeth.html✨
scmeth/json (API)
NEWS

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

Bug tracker:https://github.com/aryeelab/scmeth/issues

On BioConductor:scmeth-1.27.0(bioc 3.21)scmeth-1.26.0(bioc 3.20)

dnamethylationqualitycontrolpreprocessingsinglecellimmunooncologybioconductor-packagemethylationsingle-cell-methylation

4.70 score 5 scripts 269 downloads 1 mentions 12 exports 153 dependencies

Last updated 4 months agofrom:6017084012. Checks:1 OK, 4 NOTE, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 16 2025
R-4.5-winNOTEFeb 16 2025
R-4.5-linuxNOTEFeb 16 2025
R-4.4-winNOTEFeb 16 2025
R-4.4-macNOTEFeb 16 2025
R-4.3-winERRORJan 17 2025
R-4.3-macERRORJan 17 2025

Exports:bsConversionPlotchromosomeCoveragecoveragecpgDensitycpgDiscretizationdownsamplefeatureCoveragembiasplotmethylationDistreadmetricsrepMaskreport

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibbsseqcachemclicliprcodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsh5mreadHDF5ArrayhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplogrplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLXVectoryaml

scmeth Vignette

Divy S. Kangeyan

Rendered frommy-vignette.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2019-01-09
Started: 2017-03-28