Package: svaNUMT
Type: Package
Title: NUMT detection from structural variant calls
Version: 1.15.1
Date: 2025-07-22
Authors@R: c(
	person("Ruining", "Dong", email="lnyidrn@gmail.com", role=c("aut", "cre"), comment=c(ORCID = "0000-0003-1433-0484")))
Description: svaNUMT contains functions for detecting NUMT events from structural variant calls. 
    It takes structural variant calls in GRanges of breakend notation and identifies NUMTs by 
    nuclear-mitochondrial breakend junctions. The main function reports candidate NUMTs if there is a pair of valid insertion 
    sites found on the nuclear genome within a certain distance threshold.
    The candidate NUMTs are reported by events.
License: GPL-3 + file LICENSE
Depends: GenomicRanges, rtracklayer, VariantAnnotation,
        StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>=
        4.0)
Imports: assertthat, stringr, dplyr, methods, rlang, S4Vectors,
        Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene,
        BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>=
        2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges,
        SummarizedExperiment, rmarkdown
RoxygenNote: 7.1.2
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: DataImport, Sequencing, Annotation, Genetics,
        VariantAnnotation
BugReports: https://github.com/PapenfussLab/svaNUMT/issues
git_url: https://git.bioconductor.org/packages/svaNUMT
git_branch: devel
git_last_commit: 5cfc9e8
git_last_commit_date: 2025-07-22
Repository: Bioconductor 3.22
Date/Publication: 2025-10-07
NeedsCompilation: no
Packaged: 2025-10-07 23:24:42 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; ; 2025-10-08 06:46:00 UTC; unix
