Package: svaRetro 1.19.0

Ruining Dong

svaRetro: Retrotransposed transcript detection from structural variants

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.

Authors:Ruining Dong [aut, cre]

svaRetro_1.19.0.tar.gz
svaRetro_1.19.0.zip(r-4.7)svaRetro_1.19.0.zip(r-4.6)svaRetro_1.19.0.zip(r-4.5)
svaRetro_1.19.0.tgz(r-4.6-any)svaRetro_1.19.0.tgz(r-4.5-any)
svaRetro_1.19.0.tar.gz(r-4.7-any)svaRetro_1.19.0.tar.gz(r-4.6-any)
svaRetro_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
svaRetro/json (API)
NEWS

# Install 'svaRetro' in R:
install.packages('svaRetro', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/papenfusslab/svaretro/issues

On BioConductor:svaRetro-1.19.0(bioc 3.24)svaRetro-1.18.0(bioc 3.23)

dataimportsequencingannotationgeneticsvariantannotationcoveragevariantdetection

5.32 score 13 scripts 323 downloads 1 exports 83 dependencies

Last updated from:6a5d754c5d. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING269
linux-devel-x86_64WARNING540
source / vignettesOK437
linux-release-x86_64WARNING511
macos-release-arm64WARNING319
macos-oldrel-arm64WARNING433
windows-develWARNING426
windows-releaseWARNING385
windows-oldrelWARNING405
wasm-releaseOK231

Exports:rtDetect

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpwalignR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrStructuralVariantAnnotationSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml

svaRetro Quick Overview

Ruining Dong

Rendered fromsvaRetro.Rmdusingknitr::rmarkdownon May 10 2026.

Last update: 2026-02-18
Started: 2021-07-21