svaRetro

DOI: 10.18129/B9.bioc.svaRetro    

This is the development version of svaRetro; for the stable release version, see svaRetro.

Retrotransposed transcript detection from structural variants

Bioconductor version: Development (3.17)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("svaRetro")

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

Documentation

PDF		Reference Manual

Details

biocViews	Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection
Version	1.5.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/svaRetro
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/svaRetro
Package Short Url	https://bioconductor.org/packages/svaRetro/
Package Downloads Report	Download Stats