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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NEWS

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

Peer review:

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 226 downloads 1 mentions 12 exports 152 dependencies

Last updated 3 months agofrom:6017084012. Checks:1 OK, 4 NOTE, 2 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 17 2025
R-4.5-winNOTEJan 17 2025
R-4.5-linuxNOTEJan 17 2025
R-4.4-winNOTEJan 17 2025
R-4.4-macNOTEJan 17 2025
R-4.3-winERRORJan 17 2025
R-4.3-macERRORJan 17 2025

Exports:bsConversionPlotchromosomeCoveragecoveragecpgDensitycpgDiscretizationdownsamplefeatureCoveragembiasplotmethylationDistreadmetricsrepMaskreport

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibbsseqcachemclicliprcodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsHDF5ArrayhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplogrplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLXVectoryaml

scmeth Vignette

Divy S. Kangeyan

Rendered frommy-vignette.Rmdusingknitr::rmarkdownon Jan 17 2025.

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