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Retrotransposed transcript detection from structural variants

Bioconductor version: Release (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>

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


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

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


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 1.10.0
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
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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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Follow Installation instructions to use this package in your R session.

Source Package svaRetro_1.10.0.tar.gz
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macOS Binary (x86_64) svaRetro_1.10.0.tgz
macOS Binary (arm64) svaRetro_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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