Introduction | Prerequisites | Data import and SNP filtering | Segmentation of partially methylated domains | Identification of UMRs and LMRs
Package: MethylSeekR 1.53.0
Lukas Burger
MethylSeekR: Segmentation of Bis-seq data
This is a package for the discovery of regulatory regions from Bis-seq data
Authors:
MethylSeekR_1.53.0.tar.gz
MethylSeekR_1.53.0.zip(r-4.7)MethylSeekR_1.53.0.zip(r-4.6)MethylSeekR_1.53.0.zip(r-4.5)
MethylSeekR_1.53.0.tgz(r-4.6-any)MethylSeekR_1.53.0.tgz(r-4.5-any)
MethylSeekR_1.53.0.tar.gz(r-4.7-any)MethylSeekR_1.53.0.tar.gz(r-4.6-any)
MethylSeekR_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MethylSeekR/json (API)
| # Install 'MethylSeekR' in R: |
| install.packages('MethylSeekR', repos = c('https://bioc.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
Last updated from:354bb03239. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 246 | ||
| linux-devel-x86_64 | NOTE | 523 | ||
| source / vignettes | OK | 322 | ||
| linux-release-x86_64 | NOTE | 496 | ||
| macos-release-arm64 | NOTE | 345 | ||
| macos-oldrel-arm64 | NOTE | 314 | ||
| windows-devel | NOTE | 412 | ||
| windows-release | NOTE | 386 | ||
| windows-oldrel | NOTE | 456 | ||
| wasm-release | OK | 208 |
Exports:calculateFDRsplotAlphaDistributionOneChrplotFinalSegmentationplotPMDSegmentationreadMethylomereadSNPTableremoveSNPssavePMDSegmentssaveUMRLMRSegmentssegmentPMDssegmentUMRsLMRs
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgeneplottergenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemhsmmmimemvtnormopensslpkgconfigpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Segmentation of Bis-seq methylation data | MethylSeekR-package MethylSeekR |
| Determine false discovery rate | calculateFDRs |
| Calculate and plot alpha distribution. | plotAlphaDistributionOneChr |
| Plotting final segmentation | plotFinalSegmentation |
| Plotting the PMD Segmentation | plotPMDSegmentation |
| Load Bis-seq data | readMethylome |
| Load SNP table | readSNPTable |
| Remove CpGs overlapping SNPs | removeSNPs |
| Save PMD segments | savePMDSegments |
| Save UMR and LMR segments | saveUMRLMRSegments |
| PMD segmenter | segmentPMDs |
| Identify UMRs and LMRs | segmentUMRsLMRs |
