RgnTX

DOI: 10.18129/B9.bioc.RgnTX  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RgnTX.

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

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	RgnTX
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, MethylSeq, RNASeq, Sequencing, Software, SplicedAlignment, Transcription
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
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
LinkingTo
Suggests	BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RgnTX_1.0.0.tar.gz
Windows Binary	RgnTX_1.0.0.zip
macOS Binary (x86_64)	RgnTX_1.0.0.tgz
macOS Binary (arm64)	RgnTX_1.0.0.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