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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")):


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

svaRetro Package HTML R Script
Reference Manual PDF


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
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
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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/
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