DESCRIPTION

Package: bascule
Type: Package
Title: bascule
Version: 0.1.0
Author: Elena Buscaroli <ele.buscaroli@gmail.com>
Maintainer: Elena Buscaroli <ele.buscaroli@gmail.com>
Authors@R: c(
    person("Elena", "Buscaroli", role=c("aut", "cre"), email="ele.buscaroli@gmail.com"),
    person("Azad", "Sadr", role=c("aut", "cre"), email="azad.sadr.h@gmail.com"),
    person("Giulio", "Caravagna", role=c("aut"), email="gcaravagn@gmail.com")
    )
Description: This packages provides the bascule (Bayesian inference and clustering 
    with mutational signatures and an established catalogue) algorithm to detect 
    single-nucleotide substituion signatures in cancer. bascule provides a full 
    Bayesian formulation based on non-negative matrix factorisation, leveraging a 
    catalogue of known signatures. The tool is specifically developed to detect de 
    novo mutational signatures of any type (SBS, DBS, IDS, ...) that are different 
    from the pre-defined reference catalogue and to perform clustering of samples 
    from all the signature types jointly.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Config/reticulate:
  list(
    packages = list(
      list(package = "pybascule", pip = TRUE)
    )
  )
Imports: 
    data.table,
    ggplot2,
    gridExtra,
    reticulate,
    tidyr,
    reshape2,
    tibble,
    dplyr,
    magrittr,
    doParallel,
    cli,
    stringr,
    ggtext,
    pheatmap,
    ggplotify,
    patchwork,
    scales,
    quadprog,
    progress,
    ggh4x,
    Polychrome,
    ggrepel,
    ggsci,
    lsa,
    gtools,
    ggpubr
RoxygenNote: 7.3.1
URL: https://github.com/caravagnalab/bascule,
    https://caravagnalab.github.io/bascule/
Depends: 
    R (>= 2.10)
Suggests: 
    covr,
    knitr,
    rmarkdown
VignetteBuilder: knitr