RgnTX

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

Bioconductor version: 3.23 · Package version: 1.14.0

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.

DOI: 10.18129/B9.bioc.RgnTX

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RgnTX")

Details

Maintainer	Yue Wang <yue.wang19@student.xjtlu.edu.cn>
Author	Yue Wang [aut, cre], Jia Meng [aut]
License	Artistic-2.0
Status	Deprecated
Source branch	RELEASE_3_23
Build report	Bioconductor build system, r-universe
biocViews	AlternativeSplicing, MethylSeq, RNASeq, Sequencing, Software, SplicedAlignment, Transcription
Package Short Url	https://bioconductor.org/packages/RgnTX/

Citation

From within R, enter citation("RgnTX"):

Yue Wang, Jia Meng. RgnTX: Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity. doi:10.18129/B9.bioc.RgnTX, R package version 1.14.0, https://bioconductor.org/packages/RgnTX.

Generated from the package metadata; it may differ from the package's own citation.

Dependencies

Depends: R (>= 4.2.0)

Imports: Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene

Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)