Package: TINC
Type: Package
Title: TINC - Tumour-in-Normal contamination assessment
Version: 0.1.0
Author: Giulio Caravagna
Maintainer: Giulio Caravagna <gcaravagn@gmail.com>
Authors@R: c(
  person("Giulio", "Caravagna", role=c("aut", "cre"), email="gcaravagn@gmail.com"),
    person("Salvatore", "Milite", role=c("ctb"), email="militesalvatore@gmail.com")
    )
Description: TINC is a package that implements algorithms to determine the contamination of a bulk sequencing
  sample in the context of cancer studies (matched tumour/ normal). The contamination estimated
  by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. 
  The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it.
  The latter case is less common, and that is the main reason TINC has been developed. For this reason, the
  package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R
  packages to implement Cancer Evolution analyses.
License: GPL
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: pio, crayon, ggpubr, ggrepel, mobster, BMix, VIBER, vcfR,
        purrr, dplyr, cowplot, CNAqc, tidyr, tibble, cli, stringr,
        ggplot2
Remotes: caravagn/pio, caravagn/BMix, caravagn/mobster, caravagn/VIBER,
        caravagn/CNAqc
RoxygenNote: 7.2.3
Suggests: covr, knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/caravagnalab/TINC
BugReports: https://github.com/caravagnalab/TINC/issues
Built: R 4.4.3; ; 2025-06-02 21:06:02 UTC; unix
