MethylSeekR: Segmentation of Bis-seq data

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

Author
Lukas Burger, Dimos Gaidatzis, Dirk Schubeler and Michael Stadler
Date of publication
None
Maintainer
Lukas Burger <Lukas.Burger@fmi.ch>
License
GPL (>=2)
Version
1.14.0

View on Bioconductor

Man pages

calculateFDRs
Determine false discovery rate
MethylSeekR-package
Segmentation of Bis-seq methylation data
plotAlphaDistributionOneChr
Calculate and plot alpha distribution.
plotFinalSegmentation
Plotting final segmentation
plotPMDSegmentation
Plotting the PMD Segmentation
readMethylome
Load Bis-seq data
readSNPTable
Load SNP table
removeSNPs
Remove CpGs overlapping SNPs
savePMDSegments
Save PMD segments
saveUMRLMRSegments
Save UMR and LMR segments
segmentPMDs
PMD segmenter
segmentUMRsLMRs
Identify UMRs and LMRs

Files in this package

MethylSeekR/DESCRIPTION
MethylSeekR/NAMESPACE
MethylSeekR/R
MethylSeekR/R/PMDviterbiSegmentation.R
MethylSeekR/R/calculateAlphaDistr.R
MethylSeekR/R/calculateFDRs.R
MethylSeekR/R/createGRangesObjectPMDSegmentation.R
MethylSeekR/R/plotAlphaDistributionOneChr.R
MethylSeekR/R/plotFinalSegmentation.R
MethylSeekR/R/plotPMDSegmentation.R
MethylSeekR/R/readMethylome.R
MethylSeekR/R/readSNPTable.R
MethylSeekR/R/removeSNPs.R
MethylSeekR/R/savePMDSegments.R
MethylSeekR/R/saveUMRLMRSegments.R
MethylSeekR/R/segmentPMDs.R
MethylSeekR/R/segmentUMRsLMRs.R
MethylSeekR/R/trainPMDHMM.R
MethylSeekR/build
MethylSeekR/build/vignette.rds
MethylSeekR/inst
MethylSeekR/inst/CITATION
MethylSeekR/inst/doc
MethylSeekR/inst/doc/MethylSeekR.R
MethylSeekR/inst/doc/MethylSeekR.Rnw
MethylSeekR/inst/doc/MethylSeekR.pdf
MethylSeekR/inst/extdata
MethylSeekR/inst/extdata/Lister2009_imr90_hg18_chr22.tab
MethylSeekR/inst/extdata/SNVs_hg18_chr22.tab
MethylSeekR/man
MethylSeekR/man/MethylSeekR-package.Rd
MethylSeekR/man/calculateFDRs.Rd
MethylSeekR/man/plotAlphaDistributionOneChr.Rd
MethylSeekR/man/plotFinalSegmentation.Rd
MethylSeekR/man/plotPMDSegmentation.Rd
MethylSeekR/man/readMethylome.Rd
MethylSeekR/man/readSNPTable.Rd
MethylSeekR/man/removeSNPs.Rd
MethylSeekR/man/savePMDSegments.Rd
MethylSeekR/man/saveUMRLMRSegments.Rd
MethylSeekR/man/segmentPMDs.Rd
MethylSeekR/man/segmentUMRsLMRs.Rd
MethylSeekR/vignettes
MethylSeekR/vignettes/MethylSeekR.Rnw
MethylSeekR/vignettes/refs.bib