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RgnTX

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


Bioconductor version: Release (3.18)

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.

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

Maintainer: Yue Wang <yue.wang19 at student.xjtlu.edu.cn>

Citation (from within R, enter citation("RgnTX")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("RgnTX")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RgnTX")
RgnTX HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews AlternativeSplicing, MethylSeq, RNASeq, Sequencing, Software, SplicedAlignment, Transcription
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, graphics, IRanges, methods, regioneR, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene
System Requirements
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Suggests BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RgnTX_1.4.0.tar.gz
Windows Binary RgnTX_1.4.0.zip
macOS Binary (x86_64) RgnTX_1.4.0.tgz
macOS Binary (arm64) RgnTX_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RgnTX
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RgnTX
Bioc Package Browser https://code.bioconductor.org/browse/RgnTX/
Package Short Url https://bioconductor.org/packages/RgnTX/
Package Downloads Report Download Stats