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✨
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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 153 dependencies

Last updated 2 months agofrom:6017084012. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:bsConversionPlotchromosomeCoveragecoveragecpgDensitycpgDiscretizationdownsamplefeatureCoveragembiasplotmethylationDistreadmetricsrepMaskreport

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebslibbsseqcachemclicliprcodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdplyrDTevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablegtoolsHDF5ArrayhighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplogrplyrpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLXVectoryamlzlibbioc

scmeth Vignette

Divy S. Kangeyan

Rendered frommy-vignette.Rmdusingknitr::rmarkdownon Dec 18 2024.

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