Package: svaRetro
Type: Package
Title: Retrotransposed transcript detection from structural variants
Version: 1.15.1
Date: 2025-07-22
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, assertthat, Biostrings, stringr, dplyr,
        methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb,
        GenomicFeatures, utils
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, 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
git_url: https://git.bioconductor.org/packages/svaRetro
git_branch: devel
git_last_commit: 238534b
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-07-23
NeedsCompilation: no
Packaged: 2025-07-24 02:35:58 UTC; biocbuild
Author: Ruining Dong [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1433-0484>)
Maintainer: Ruining Dong <lnyidrn@gmail.com>
Built: R 4.5.1; ; 2025-07-24 14:20:59 UTC; windows
