Package: RAIDS
Type: Package
Title: Robust Ancestry Inference using Data Synthesis
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: 1.9.0
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, dplyr,
        Rsamtools
Imports: S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi,
        methods, class, pROC, IRanges, AnnotationFilter, rlang,
        VariantAnnotation, MatrixGenerics, ggplot2, stringr
Suggests: testthat, knitr, rmarkdown, BiocStyle, withr, Seqinfo,
        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
Config/pak/sysreqs: cmake libglpk-dev make libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:25:36 UTC
RemoteUrl: https://github.com/bioc/RAIDS
RemoteRef: HEAD
RemoteSha: 27cee949ddef4eb263ee9365710af0dc8380e747
Packaged: 2026-01-09 21:43:33 UTC; root
Author: Pascal Belleau [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-0802-1071>),
  Astrid Deschênes [aut] (ORCID: <https://orcid.org/0000-0001-7846-6749>),
  David A. Tuveson [aut] (ORCID: <https://orcid.org/0000-0002-8017-2712>),
  Alexander Krasnitz [aut]
Maintainer: Pascal Belleau <pascal_belleau@hotmail.com>
Built: R 4.6.0; ; 2026-01-09 21:50:04 UTC; windows
