DESCRIPTION

Type: Package
Package: gcap
Title: Gene-level Circular Amplicon Prediction
Version: 1.2.0
Authors@R: 
    person("Shixiang", "Wang", , "w_shixiang@163.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-9855-7357"))
Description: Provides data processing pipeline feeding paired bam files
    (or allele-specific copy number data) and XGBOOST model for predicting
    tumor circular amplicons (also known as ecDNA) in gene level.
License: Non-Commercial Academic License + file LICENSE
URL: https://github.com/ShixiangWang/gcap,
    https://shixiangwang.github.io/gcap/
BugReports: https://github.com/ShixiangWang/gcap/issues
Depends: 
    ASCAT (>= 3.0.0),
    R (>= 3.5),
    sigminer (>= 2.1.1)
Imports:
    cli (>= 3.1.0),
    data.table,
    GetoptLong,
    glue,
    lgr,
    magrittr,
    mltools,
    purrr,
    quadprog,
    R6,
    rappdirs,
    Rcpp,
    stats,
    uuid,
    xgboost
Suggests: 
    BiocManager,
    copynumber,
    facets,
    IDConverter (>= 0.3.0),
    PRROC,
    sequenza,
    testthat (>= 3.0.0),
    utils
LinkingTo: 
    Rcpp
Remotes: 
    git::https://bitbucket.org/sequenzatools/sequenza.git@master,
    github::VanLoo-lab/ascat/ASCAT,
    github::ShixiangWang/copynumber,
    github::ShixiangWang/facets,
    github::ShixiangWang/IDConverter
biocViews:
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
    "roxytest::testthat_roclet"))
RoxygenNote: 7.3.1