DESCRIPTION

Package: svaNUMT
Type: Package
Title: NUMT detection from structural variant calls
Version: 1.3.0
Date: 2022-03-07
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,    
    GenomeInfoDb,
    S4Vectors,
    GenomicFeatures
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