Package: RgnTX 1.9.0

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_1.9.0.tar.gz
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RgnTX.pdf |RgnTX.html✨
RgnTX/json (API)
NEWS

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

Peer review:

On BioConductor:RgnTX-1.9.0(bioc 3.21)RgnTX-1.8.0(bioc 3.20)

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

alternativesplicingsequencingrnaseqmethylseqtranscriptionsplicedalignment

4.00 score 6 scripts 150 downloads 26 exports 90 dependencies

Last updated 3 months agofrom:c0f12080a8. Checks:7 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 20 2025
R-4.5-winOKJan 20 2025
R-4.5-linuxOKJan 20 2025
R-4.4-winOKJan 20 2025
R-4.4-macOKJan 20 2025
R-4.3-winOKJan 20 2025
R-4.3-macOKJan 20 2025

Exports:calculateShiftdistanceTxextractRegionsgetPermSpaceByFeaturesgetPermSpaceByTxIDgetPermSpaceByTypegetStopCodongetTransInfoGRanges2GRangesListGRangesList2GRangesoverlapCountsTxoverlapCountsTxIAoverlapWidthTxpermTestTxpermTestTx_customAllpermTestTx_customPickpermTestTxIApermTestTxIA_customPickplotPermResultsplotShiftedZScoreTxrandomizeFeaturesTxrandomizeFeaturesTxIArandomizeTransByOrderrandomizeTxshiftedZScoreTxshiftTx

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlregioneRrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

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

Yue Wang, Jia Meng

Rendered fromRgnTX.Rmdusingknitr::rmarkdownon Jan 20 2025.

Last update: 2022-05-27
Started: 2022-04-04