DESCRIPTION

Package: svaRetro
Type: Package
Title: Retrotransposed transcript detection from structural variants
Version: 1.3.0
Date: 2022-02-10
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,
    GenomicFeatures,
    GenomeInfoDb,
    S4Vectors,
    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