Package: msgbsR 1.31.0
Benjamin Mayne
msgbsR: msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Pipeline for the anaysis of a MS-GBS experiment.
Authors:
msgbsR_1.31.0.tar.gz
msgbsR_1.31.0.zip(r-4.5)msgbsR_1.31.0.zip(r-4.4)msgbsR_1.31.0.zip(r-4.3)
msgbsR_1.31.0.tgz(r-4.4-any)msgbsR_1.31.0.tgz(r-4.3-any)
msgbsR_1.31.0.tar.gz(r-4.5-noble)msgbsR_1.31.0.tar.gz(r-4.4-noble)
msgbsR_1.31.0.tgz(r-4.4-emscripten)msgbsR_1.31.0.tgz(r-4.3-emscripten)
msgbsR.pdf |msgbsR.html✨
msgbsR/json (API)
| # Install 'msgbsR' in R: |
| install.packages('msgbsR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- cuts - A GRanges object of differentially methylated MspI cut sites on chromosome 20 in Rat from a MS-GBS experiment.
- ratdata - Read counts of potential MspI cut sites from a MS-GBS experiment of prostates from rats
- ratdata2 - Read counts of correct MspI cut sites from a MS-GBS experiment of prostates from rats
On BioConductor:msgbsR-1.31.0(bioc 3.21)msgbsR-1.30.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydifferentialmethylationdataimportepigeneticsmethylseq
Last updated 23 days agofrom:c7b70de6ef. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | WARNING | Nov 18 2024 |
| R-4.5-linux | WARNING | Nov 18 2024 |
| R-4.4-win | WARNING | Nov 18 2024 |
| R-4.4-mac | WARNING | Nov 18 2024 |
| R-4.3-win | WARNING | Nov 18 2024 |
| R-4.3-mac | WARNING | Nov 18 2024 |
Exports:checkCutsdiffMethplotCircosplotCountsrawCounts
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyreasyRNASeqedgeRensembldbevaluatefansifarverfastmapfilelockfontawesomeforcatsforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagenomeIntervalsGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsgluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2hwriterinterpintervalsIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitLSDmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslOrganismDbipatchworkpillarpkgconfigplogrplyrpngprettyunitsprogressProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| checkCuts | checkCuts |
| A GRanges object of differentially methylated MspI cut sites on chromosome 20 in Rat from a MS-GBS experiment. | cuts |
| diffMeth | diffMeth |
| msgbsR | msgbsR-package msgbsR |
| plotCircos | plotCircos |
| plotCounts | plotCounts |
| Read counts of potential MspI cut sites from a MS-GBS experiment of prostates from rats | ratdata |
| Read counts of correct MspI cut sites from a MS-GBS experiment of prostates from rats | ratdata2 |
| rawCounts | rawCounts |