Package: svaNUMT
Type: Package
Title: NUMT detection from structural variant calls
Version: 1.19.0
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
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 12:56:28 UTC
RemoteUrl: https://github.com/bioc/svaNUMT
RemoteRef: HEAD
RemoteSha: 66c92cc7b19008e4b62dd28dd4dab9079355463b
NeedsCompilation: no
Packaged: 2026-07-04 12:06:48 UTC; root
Author: Ruining Dong [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1433-0484>)
Maintainer: Ruining Dong <lnyidrn@gmail.com>