DESCRIPTION

Package: RAIDS
Type: Package
Title: Accurate Inference of Genetic Ancestry from Cancer Sequences
Description: This package implements specialized algorithms that enable
    genetic ancestry inference from various cancer sequences sources (RNA,
    Exome and Whole-Genome sequences). This package also implements a
    simulation algorithm that generates synthetic cancer-derived data. 
    This code and analysis pipeline was designed and developed for the
    following publication: Belleau, P et al. Genetic Ancestry Inference from 
    Cancer-Derived Molecular Data across Genomic and Transcriptomic 
    Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.
Version: 1.3.3
Authors@R: c(person("Pascal", "Belleau", email="pascal_belleau@hotmail.com",
    role=c("cre", "aut"), comment = c(ORCID = "0000-0002-0802-1071")),
    person("Astrid", "Deschênes", email="adeschen@hotmail.com",
    role=c("aut"), comment = c(ORCID = "0000-0001-7846-6749")),
    person(given="David A.", family="Tuveson",
    email="dtuveson@cshl.edu", 
    role=c("aut"), comment=c(ORCID="0000-0002-8017-2712")),
    person("Alexander", "Krasnitz", email="krasnitz@cshl.edu",
    role=c("aut")))
License: Apache License (>= 2)
Encoding: UTF-8
NeedsCompilation: no
VignetteBuilder: knitr
Depends: R (>= 4.2.0),
    gdsfmt,
    SNPRelate,
    stats,
    utils,
    GENESIS
Imports: S4Vectors,
    GenomicRanges,
    ensembldb,
    BSgenome,
    AnnotationDbi,
    methods,
    class,
    pROC,
    IRanges,
    AnnotationFilter,
    rlang,
    VariantAnnotation,
    MatrixGenerics,
    ggplot2,
    stringr
Suggests: testthat,
    knitr,
    rmarkdown,
    BiocStyle,
    withr,
    GenomeInfoDb,
    BSgenome.Hsapiens.UCSC.hg38,
    EnsDb.Hsapiens.v86
BugReports: https://github.com/KrasnitzLab/RAIDS/issues
URL: https://krasnitzlab.github.io/RAIDS/
biocViews: Genetics, Software, Sequencing, WholeGenome, PrincipalComponent, 
    GeneticVariability, DimensionReduction, BiocViews
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2