Package: MethylSeekR 1.52.0

Lukas Burger

MethylSeekR: Segmentation of Bis-seq data

This is a package for the discovery of regulatory regions from Bis-seq data

Authors:Lukas Burger, Dimos Gaidatzis, Dirk Schubeler and Michael Stadler

MethylSeekR_1.52.0.tar.gz
MethylSeekR_1.52.0.zip(r-4.7)MethylSeekR_1.52.0.zip(r-4.6)MethylSeekR_1.52.0.zip(r-4.5)
MethylSeekR_1.52.0.tgz(r-4.6-any)MethylSeekR_1.52.0.tgz(r-4.5-any)
MethylSeekR_1.52.0.tar.gz(r-4.7-any)MethylSeekR_1.52.0.tar.gz(r-4.6-any)
MethylSeekR_1.52.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MethylSeekR/json (API)

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

On BioConductor:MethylSeekR-1.53.0(bioc 3.24)MethylSeekR-1.52.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencingmethylseqdnamethylation

4.55 score 44 scripts 567 downloads 33 mentions 11 exports 74 dependencies

Last updated from:763e1ee60a (on RELEASE_3_23). Checks:9 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR272
linux-devel-x86_64ERROR403
source / vignettesERROR378
linux-release-x86_64ERROR421
macos-release-arm64ERROR270
macos-oldrel-arm64ERROR270
windows-develERROR373
windows-releaseERROR354
windows-oldrelERROR365
wasm-releaseOK214

Exports:calculateFDRsplotAlphaDistributionOneChrplotFinalSegmentationplotPMDSegmentationreadMethylomereadSNPTableremoveSNPssavePMDSegmentssaveUMRLMRSegmentssegmentPMDssegmentUMRsLMRs

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgeneplottergenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemhsmmmimemvtnormopensslpkgconfigpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLxtableXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Segmentation of Bis-seq methylation dataMethylSeekR-package MethylSeekR
Determine false discovery ratecalculateFDRs
Calculate and plot alpha distribution.plotAlphaDistributionOneChr
Plotting final segmentationplotFinalSegmentation
Plotting the PMD SegmentationplotPMDSegmentation
Load Bis-seq datareadMethylome
Load SNP tablereadSNPTable
Remove CpGs overlapping SNPsremoveSNPs
Save PMD segmentssavePMDSegments
Save UMR and LMR segmentssaveUMRLMRSegments
PMD segmentersegmentPMDs
Identify UMRs and LMRssegmentUMRsLMRs