Package: bascule
Type: Package
Title: bascule
Version: 1.0.0
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: 7.3.2
URL: https://github.com/caravagnalab/bascule,
        https://caravagnalab.github.io/bascule/
Depends: R (>= 3.5)
Suggests: survminer, survival, forestmodel, covr, knitr, rmarkdown
VignetteBuilder: knitr
Built: R 4.4.3; ; 2025-06-25 03:07:02 UTC; unix
