Package: RgnTX 1.14.0

Yue Wang

RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity

RgnTX allows the integration of transcriptome annotations so as to model the complex alternative splicing patterns. It supports the testing of transcriptome elements without clear isoform association, which is often the real scenario due to technical limitations. It involves functions that do permutaion test for evaluating association between features and transcriptome regions.

Authors:Yue Wang [aut, cre], Jia Meng [aut]

RgnTX_1.14.0.tar.gz
RgnTX_1.14.0.zip(r-4.7)RgnTX_1.14.0.zip(r-4.6)RgnTX_1.14.0.zip(r-4.5)
RgnTX_1.14.0.tgz(r-4.6-any)RgnTX_1.14.0.tgz(r-4.5-any)
RgnTX_1.14.0.tar.gz(r-4.7-any)RgnTX_1.14.0.tar.gz(r-4.6-any)
RgnTX_1.14.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
RgnTX/json (API)
NEWS

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

alternativesplicingsequencingrnaseqmethylseqtranscriptionsplicedalignment

2.30 score 8 scripts 235 downloads 26 exports 81 dependencies

Last updated from:299af2aa50 (on RELEASE_3_23). Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING288
linux-devel-x86_64ERROR546
source / vignettesERROR379
linux-release-x86_64ERROR481
macos-release-arm64ERROR428
macos-oldrel-arm64ERROR353
windows-develERROR405
windows-releaseERROR408
windows-oldrelERROR399
wasm-releaseOK162

Exports:calculateShiftdistanceTxextractRegionsgetPermSpaceByFeaturesgetPermSpaceByTxIDgetPermSpaceByTypegetStopCodongetTransInfoGRanges2GRangesListGRangesList2GRangesoverlapCountsTxoverlapCountsTxIAoverlapWidthTxpermTestTxpermTestTx_customAllpermTestTx_customPickpermTestTxIApermTestTxIA_customPickplotPermResultsplotShiftedZScoreTxrandomizeFeaturesTxrandomizeFeaturesTxIArandomizeTransByOrderrandomizeTxshiftedZScoreTxshiftTx

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RColorBrewerRCurlregioneRrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySummarizedExperimentsysTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsvctrsviridisLitewithrXMLXVectoryaml