svaRetro

DOI: 10.18129/B9.bioc.svaRetro  

Retrotransposed transcript detection from structural variants

Bioconductor version: Release (3.16)

svaRetro contains functions for detecting retrotransposed transcripts (RTs) from structural variant calls. It takes structural variant calls in GRanges of breakend notation and identifies RTs by exon-exon junctions and insertion sites. The candidate RTs are reported by events and annotated with information of the inserted transcripts.

Author: Ruining Dong [aut, cre]

Maintainer: Ruining Dong <lnyidrn at gmail.com>

Installation

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

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

BiocManager::install("svaRetro")

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("svaRetro")

 

HTML	R Script	svaRetro Package
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3 + file LICENSE
Depends	GenomicRanges, rtracklayer, BiocGenerics, StructuralVariantAnnotation, R (>= 4.0)
Imports	VariantAnnotation, assertthat, Biostrings, stringr, dplyr, methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils
LinkingTo
Suggests	TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/PapenfussLab/svaRetro/issues
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	svaRetro_1.4.0.tar.gz
Windows Binary	svaRetro_1.4.0.zip
macOS Binary (x86_64)	svaRetro_1.4.0.tgz
macOS Binary (arm64)	svaRetro_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/svaRetro
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/svaRetro
Bioc Package Browser	https://code.bioconductor.org/browse/svaRetro/
Package Short Url	https://bioconductor.org/packages/svaRetro/
Package Downloads Report	Download Stats