Package: rnaEditr 1.17.0

Lanyu Zhang

rnaEditr: Statistical analysis of RNA editing sites and hyper-editing regions

RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.

Authors:Lanyu Zhang [aut, cre], Gabriel Odom [aut], Tiago Silva [aut], Lissette Gomez [aut], Lily Wang [aut]

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rnaEditr.pdf |rnaEditr.html
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NEWS

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

Bug tracker:https://github.com/transbioinfolab/rnaeditr/issues

Datasets:
  • rnaedit_df - Example breast cancer RNA editing dataset.
  • t_rnaedit_df - Transposed breast cancer example dataset.

On BioConductor:rnaEditr-1.17.0(bioc 3.21)rnaEditr-1.16.0(bioc 3.20)

genetargetepigeneticsdimensionreductionfeatureextractionregressionsurvivalrnaseq

4.48 score 3 stars 9 scripts 242 downloads 27 exports 129 dependencies

Last updated 5 months agofrom:a074827a5d. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 13 2025
R-4.5-winWARNINGMar 13 2025
R-4.5-macWARNINGMar 13 2025
R-4.5-linuxWARNINGMar 13 2025
R-4.4-winWARNINGMar 13 2025
R-4.4-macWARNINGMar 13 2025
R-4.4-linuxWARNINGMar 13 2025
R-4.3-winWARNINGMar 13 2025
R-4.3-macWARNINGMar 13 2025

Exports:AddMetaDataAllCloseByRegionsAllCoeditedRegionsAnnotateResultsCountSamplesPerGroupCreateEditingTableCreateOutputDFCreateRdropFindCorrelatedRegionsGetMinPairwiseCorGetSitesLocationsMakeModelFormulaMarkCoeditedSitesMaxSitesMeanSitesMedianSitesOrderSitesByLocationPC1SitesPlotEditingCorrelationsSingleCloseByRegionSingleCoeditedRegionSitesToRegionSummarizeAllRegionsSummarizeSingleRegionTestAssociationsTestSingleRegionTransformToGR

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbroombumphuntercachemclicliprcodetoolscorrplotcpp11crayoncurlDBIDelayedArraydigestdoRNGdplyrfansifastmapforcatsforeachformatRformula.toolsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesglmnetgluehavenhmshttrIRangesiteratorsjomojsonliteKEGGRESTlambda.rlatticelifecyclelimmalme4locfitlogistfmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicemimeminqamitmlnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rbibutilsRcppRcppEigenRCurlRdpackreadrreformulasrestfulrRhtslibrjsonrlangrngtoolsrpartRsamtoolsRSQLitertracklayerS4ArraysS4VectorsshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbucminfUCSC.utilsutf8vctrsvroomwithrXMLXVectoryaml

Introduction to rnaEditr

Rendered fromintroduction_to_rnaEditr.Rmdusingknitr::rmarkdownon Mar 13 2025.

Last update: 2020-10-07
Started: 2020-09-26