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svaRetro

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

Retrotransposed transcript detection from structural variants


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

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

browseVignettes("svaRetro")
svaRetro Package HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, Coverage, DataImport, Genetics, Sequencing, Software, VariantAnnotation, VariantDetection
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL
Bug Reports https://github.com/PapenfussLab/svaRetro/issues
See More
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges, circlize, tictoc, IRanges, stats, SummarizedExperiment, rmarkdown
Linking To
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Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package svaRetro_1.9.0.tar.gz
Windows Binary svaRetro_1.9.0.zip
macOS Binary (x86_64) svaRetro_1.9.0.tgz
macOS Binary (arm64) svaRetro_1.9.0.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