Package: msgbsR 1.37.0
Benjamin Mayne
msgbsR: msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Pipeline for the anaysis of a MS-GBS experiment.
Authors:
msgbsR_1.37.0.tar.gz
msgbsR_1.37.0.zip(r-4.7-any)msgbsR_1.37.0.zip(r-4.6-any)msgbsR_1.37.0.zip(r-4.5-any)
msgbsR_1.37.0.tgz(r-4.6-any)msgbsR_1.37.0.tgz(r-4.5-any)
msgbsR_1.37.0.tar.gz(r-4.7-any)msgbsR_1.37.0.tar.gz(r-4.6-any)
msgbsR_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.37.0(bioc 3.24)msgbsR-1.36.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydifferentialmethylationdataimportepigeneticsmethylseq
Last updated from:9f01b78a20. Checks:9 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 274 | ||
| linux-devel | ERROR | 523 | ||
| source / vignettes | ERROR | 402 | ||
| linux-release | ERROR | 574 | ||
| macos-release | ERROR | 516 | ||
| macos-oldrel | ERROR | 459 | ||
| windows-devel | ERROR | 484 | ||
| windows-release | ERROR | 456 | ||
| windows-oldrel | ERROR | 472 | ||
| wasm-release | OK | 243 |
Exports:checkCutsdiffMethplotCircosplotCountsrawCounts
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarillocliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyreasyRNASeqedgeRensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbgenomeIntervalsGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2gluegraphgridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2hwriterinterpintervalsIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalocfitLSDmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbipillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfoShortReadsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml
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 |