Package: svaNUMT
Type: Package
Title: NUMT detection from structural variant calls
Version: 1.0.0
Date: 2021-03-09
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
Depends: GenomicRanges, rtracklayer, VariantAnnotation,
        StructuralVariantAnnotation, BiocGenerics, R (>= 4.0)
Imports: assertthat, Biostrings, stringr, dplyr, methods, rlang,
        GenomeInfoDb, S4Vectors, GenomicFeatures
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools,
        testthat (>= 2.1.0), roxygen2, knitr, plyranges, circlize,
        tictoc, IRanges, SummarizedExperiment, rmarkdown
RoxygenNote: 7.1.1
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: RELEASE_3_14
git_last_commit: 2fc3188
git_last_commit_date: 2021-10-26
Date/Publication: 2021-10-26
NeedsCompilation: no
Packaged: 2021-10-27 04:18:19 UTC; biocbuild
Author: Ruining Dong [aut, cre] (<https://orcid.org/0000-0003-1433-0484>)
Maintainer: Ruining Dong <lnyidrn@gmail.com>
Built: R 4.1.1; ; 2021-10-27 13:42:47 UTC; windows
