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 122 downloads 26 exports 91 dependencies

Last updated 2 months agofrom:c0f12080a8. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKDec 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKDec 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKDec 21 2024

Exports:calculateShiftdistanceTxextractRegionsgetPermSpaceByFeaturesgetPermSpaceByTxIDgetPermSpaceByTypegetStopCodongetTransInfoGRanges2GRangesListGRangesList2GRangesoverlapCountsTxoverlapCountsTxIAoverlapWidthTxpermTestTxpermTestTx_customAllpermTestTx_customPickpermTestTxIApermTestTxIA_customPickplotPermResultsplotShiftedZScoreTxrandomizeFeaturesTxrandomizeFeaturesTxIArandomizeTransByOrderrandomizeTxshiftedZScoreTxshiftTx

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArrayfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngR6RColorBrewerRCurlregioneRrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleTxDb.Hsapiens.UCSC.hg19.knownGeneUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

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

Yue Wang, Jia Meng

Rendered fromRgnTX.Rmdusingknitr::rmarkdownon Dec 21 2024.

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