Package: svaRetro
Type: Package
Title: Retrotransposed transcript detection from structural variants
Version: 1.19.0
Date: 2026-02-18
Authors@R: 
    c(person(given = "Ruining",
             family = "Dong",
             role = c("aut", "cre"),
             email = "lnyidrn@gmail.com",
             comment = c(ORCID = "0000-0003-1433-0484")))
Description: 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.
License: GPL-3 + file LICENSE
Depends: GenomicRanges, rtracklayer, BiocGenerics,
        StructuralVariantAnnotation, R (>= 4.0)
Imports: VariantAnnotation, AnnotationDbi, assertthat, Biostrings,
        stringr, dplyr, methods, rlang, S4Vectors, Seqinfo,
        GenomeInfoDb, GenomicFeatures, utils
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, ggplot2,
        devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle,
        plyranges, circlize, tictoc, IRanges, stats,
        SummarizedExperiment, rmarkdown
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: DataImport, Sequencing, Annotation, Genetics,
        VariantAnnotation, Coverage, VariantDetection
BugReports: https://github.com/PapenfussLab/svaRetro/issues
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:48 UTC
RemoteUrl: https://github.com/bioc/svaRetro
RemoteRef: HEAD
RemoteSha: 6a5d754c5d5483237e572c0102dbeb7c083539b1
NeedsCompilation: no
Packaged: 2026-05-10 09:38:11 UTC; root
Author: Ruining Dong [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1433-0484>)
Maintainer: Ruining Dong <lnyidrn@gmail.com>
Built: R 4.6.0; ; 2026-05-10 09:40:57 UTC; windows
