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✨
DESCRIPTION |NEWS
card.svg |card.png
svaRetro/json (API)

# 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)

dataimport sequencing annotation genetics variantannotation coverage variantdetection

5.20 score 8 scripts 324 downloads 1 exports 83 dependencies

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

Target	Result	Time
bioc-checks	WARNING	269
linux-devel-x86_64	WARNING	582
source / vignettes	OK	382
linux-release-x86_64	WARNING	526
macos-release-arm64	WARNING	373
macos-oldrel-arm64	WARNING	343
windows-devel	WARNING	456
windows-release	WARNING	395
windows-oldrel	WARNING	436
wasm-release	OK	229

Exports:rtDetect

Dependencies:abind AnnotationDbi askpass assertthat BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png pwalign R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr StructuralVariantAnnotation SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml

svaRetro Quick Overview

Rendered fromsvaRetro.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Replaces the NA values in a with corresponding values in b	%na%
Uses b if a is NULL	%null%
Detecting retrotranscript insertion in nuclear genomes.	rtDetect
svaRetro: a package for retrotransposed transcript detection	svaRetro