1 Installation | 2 Datasets | 3 Site-specific analysis | 3.1 Testing all edited sites | 3.2 Annotate results | 4 Region-based analysis | 4.1 Input regions | 4.2 Find close-by regions | 4.3 Find co-edited regions | 4.4 Summarize all regions | 4.5 Test all regions | 4.6 Annotate results | 5 Further examples of function TestAssociations in rnaEditr | 6 Session information
Package: rnaEditr 1.23.0
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:
rnaEditr_1.23.0.tar.gz
rnaEditr_1.23.0.zip(r-4.7)rnaEditr_1.23.0.zip(r-4.6)rnaEditr_1.23.0.zip(r-4.5)
rnaEditr_1.23.0.tgz(r-4.6-any)rnaEditr_1.23.0.tgz(r-4.5-any)
rnaEditr_1.23.0.tar.gz(r-4.7-any)rnaEditr_1.23.0.tar.gz(r-4.6-any)
rnaEditr_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rnaEditr/json (API)
| # 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-1.23.0(bioc 3.24)rnaEditr-1.22.0(bioc 3.23)
genetargetepigeneticsdimensionreductionfeatureextractionregressionsurvivalrnaseq
Last updated from:121a510af9. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 279 | ||
| linux-devel-x86_64 | WARNING | 420 | ||
| source / vignettes | OK | 329 | ||
| linux-release-x86_64 | WARNING | 468 | ||
| macos-release-arm64 | WARNING | 302 | ||
| macos-oldrel-arm64 | WARNING | 251 | ||
| windows-devel | WARNING | 363 | ||
| windows-release | WARNING | 259 | ||
| windows-oldrel | WARNING | 317 | ||
| wasm-release | OK | 229 |
Exports:AddMetaDataAllCloseByRegionsAllCoeditedRegionsAnnotateResultsCountSamplesPerGroupCreateEditingTableCreateOutputDFCreateRdropFindCorrelatedRegionsGetMinPairwiseCorGetSitesLocationsMakeModelFormulaMarkCoeditedSitesMaxSitesMeanSitesMedianSitesOrderSitesByLocationPC1SitesPlotEditingCorrelationsSingleCloseByRegionSingleCoeditedRegionSitesToRegionSummarizeAllRegionsSummarizeSingleRegionTestAssociationsTestSingleRegionTransformToGR
Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootbroombumphuntercachemcigarilloclicliprcodetoolscorrplotcpp11crayoncurlDBIDelayedArraydigestdoRNGdplyrfastmapforcatsforeachformatRformula.toolsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesglmnetgluehavenhmshttrIRangesiteratorsjomojsonliteKEGGRESTlambda.rlatticelifecyclelimmalme4locfitlogistfmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmicemimeminqamitmlnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rbibutilsRcppRcppEigenRCurlRdpackreadrreformulasrestfulrRhtslibrjsonrlangrngtoolsrpartRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfoshapesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbucminfutf8vctrsvroomwithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract clusters of RNA editing sites located closely in genomic regions. | AllCloseByRegions |
| Extracts contiguous co-edited genomic regions from input genomic regions . | AllCoeditedRegions |
| Add Annotations to site-specific or region-based analysis results. | AnnotateResults |
| Convert RNA editing matrix into a special data frame with class 'rnaEdit_df'. | CreateEditingTable |
| Example breast cancer RNA editing dataset. | rnaedit_df |
| Summarize RNA editing levels from multiple sites in regions. | SummarizeAllRegions |
| Transposed breast cancer example dataset. | t_rnaedit_df |
| Test associations between phenotype and RNA editing levels. | TestAssociations |
| Transform gene symbols or region ranges into GRanges object. | TransformToGR |
