RgnTX
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
Bioconductor version: Release (3.19)
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("RgnTX")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, MethylSeq, RNASeq, Sequencing, Software, SplicedAlignment, Transcription |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 | |
| URL |
See More
| Suggests | BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RgnTX_1.6.0.tar.gz |
| Windows Binary (x86_64) | RgnTX_1.6.0.zip |
| macOS Binary (x86_64) | RgnTX_1.6.0.tgz |
| macOS Binary (arm64) | RgnTX_1.6.0.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 |