Package: RNAmodR.RiboMethSeq 1.27.0

Felix G.M. Ernst

RNAmodR.RiboMethSeq: Detection of 2'-O methylations by RiboMethSeq

RNAmodR.RiboMethSeq implements the detection of 2'-O methylations on RNA from experimental data generated with the RiboMethSeq protocol. The package builds on the core functionality of the RNAmodR package to detect specific patterns of the modifications in high throughput sequencing data.

Authors:Felix G.M. Ernst [aut, cre], Denis L.J. Lafontaine [ctb, fnd]

RNAmodR.RiboMethSeq_1.27.0.tar.gz
RNAmodR.RiboMethSeq_1.27.0.zip(r-4.7-any)RNAmodR.RiboMethSeq_1.27.0.zip(r-4.6-any)RNAmodR.RiboMethSeq_1.27.0.zip(r-4.5-any)
RNAmodR.RiboMethSeq_1.27.0.tgz(r-4.6-any)RNAmodR.RiboMethSeq_1.27.0.tgz(r-4.5-any)
RNAmodR.RiboMethSeq_1.27.0.tar.gz(r-4.7-any)RNAmodR.RiboMethSeq_1.27.0.tar.gz(r-4.6-any)
RNAmodR.RiboMethSeq_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RNAmodR.RiboMethSeq/json (API)

# Install 'RNAmodR.RiboMethSeq' in R:
install.packages('RNAmodR.RiboMethSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/felixernst/rnamodr.ribomethseq/issues

Datasets:
  • msrms - Example data in the RNAmodR.RiboMethSeq package

On BioConductor:RNAmodR.RiboMethSeq-1.27.0(bioc 3.24)RNAmodR.RiboMethSeq-1.26.0(bioc 3.23)

softwareworkflowstepvisualizationsequencingbioconductormodificationsribomethseqrnarnamodr

3.30 score 1 stars 9 scripts 510 downloads 8 exports 154 dependencies

Last updated from:6f2e7546b9. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING221
linux-develERROR582
source / vignettesERROR361
linux-releaseERROR516
macos-releaseERROR404
macos-oldrelERROR447
windows-develERROR475
windows-releaseERROR625
windows-oldrelERROR626
wasm-releaseOK172

Exports:aggregateDatafindModgetDataTrackModRiboMethSeqModSetRiboMethSeqplotDataplotDataByCoordsettings<-

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmatecigarillocliclustercodetoolscolorRampscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegplotsgridExtragtablegtoolsGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2interpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeModstringsnnetopensslpillarpkgconfigplyrpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownRNAmodRROCRrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrxfunXMLxml2XVectoryaml

Readme and manuals

Help Manual

Help pageTopics
ModRiboMethSeq class to analyze RiboMethSeq dataModRiboMethSeq ModRiboMethSeq-class ModSetRiboMethSeq ModSetRiboMethSeq-class RiboMethSeq
Functions for ModRiboMethSeqaggregate aggregateData,ModRiboMethSeq-method findMod,ModRiboMethSeq-method getDataTrack,ModRiboMethSeq-method modify ModRiboMethSeq-functions plotData plotData,ModRiboMethSeq-method plotData,ModSetRiboMethSeq-method plotDataByCoord plotDataByCoord,ModRiboMethSeq,GRanges-method plotDataByCoord,ModSetRiboMethSeq,GRanges-method settings settings<-,ModRiboMethSeq-method
RNAmodR.RiboMethSeqRNAmodR.RiboMethSeq
Example data in the RNAmodR.RiboMethSeq packagemsrms RNAmodR.RiboMethSeq-datasets