Package: MethylSeekR 1.47.0
Lukas Burger
MethylSeekR: Segmentation of Bis-seq data
This is a package for the discovery of regulatory regions from Bis-seq data
Authors:
MethylSeekR_1.47.0.tar.gz
MethylSeekR_1.47.0.zip(r-4.5)MethylSeekR_1.47.0.zip(r-4.4)MethylSeekR_1.47.0.zip(r-4.3)
MethylSeekR_1.47.0.tgz(r-4.4-any)MethylSeekR_1.47.0.tgz(r-4.3-any)
MethylSeekR_1.47.0.tar.gz(r-4.5-noble)MethylSeekR_1.47.0.tar.gz(r-4.4-noble)
MethylSeekR_1.47.0.tgz(r-4.4-emscripten)MethylSeekR_1.47.0.tgz(r-4.3-emscripten)
MethylSeekR.pdf |MethylSeekR.html✨
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-1.47.0(bioc 3.21)MethylSeekR-1.46.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingmethylseqdnamethylation
Last updated 23 days agofrom:bd272df9a1. Checks:OK: 1 WARNING: 4 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | WARNING | Nov 08 2024 |
| R-4.5-linux | WARNING | Nov 08 2024 |
| R-4.4-win | WARNING | Nov 08 2024 |
| R-4.4-mac | NOTE | Nov 08 2024 |
| R-4.3-win | WARNING | Nov 08 2024 |
| R-4.3-mac | NOTE | Nov 08 2024 |
Exports:calculateFDRsplotAlphaDistributionOneChrplotFinalSegmentationplotPMDSegmentationreadMethylomereadSNPTableremoveSNPssavePMDSegmentssaveUMRLMRSegmentssegmentPMDssegmentUMRsLMRs
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemhsmmmimemvtnormopensslpkgconfigplogrpngR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLxtableXVectoryamlzlibbioc
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 |
