Package: svaRetro 1.18.0

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_1.18.0.tar.gz
svaRetro_1.18.0.zip(r-4.7)svaRetro_1.18.0.zip(r-4.6)svaRetro_1.18.0.zip(r-4.5)
svaRetro_1.18.0.tgz(r-4.6-any)svaRetro_1.18.0.tgz(r-4.5-any)
svaRetro_1.18.0.tar.gz(r-4.7-any)svaRetro_1.18.0.tar.gz(r-4.6-any)
svaRetro_1.18.0.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-release.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 333 downloads 1 exports 82 dependencies

Last updated from:c3370c7ee5 (on RELEASE_3_23). Checks:8 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING271
linux-devel-x86_64WARNING417
source / vignettesOK394
linux-release-x86_64WARNING662
macos-release-arm64WARNING415
macos-oldrel-arm64WARNING327
windows-develWARNING427
windows-releaseWARNING411
windows-oldrelWARNING413
wasm-releaseOK269

Exports:rtDetect

Dependencies:abindAnnotationDbiaskpassassertthatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpwalignR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrStructuralVariantAnnotationSummarizedExperimentsystibbletidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLXVectoryaml

svaRetro Quick Overview

Ruining Dong

Rendered fromsvaRetro.Rmdusingknitr::rmarkdownon May 30 2026.

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