Package: ICBioMark
Title: Data-Driven Design of Targeted Gene Panels for Estimating
        Immunotherapy Biomarkers
Version: 0.1.4
Authors@R: 
    c(person(given = "Jacob R.",
           family = "Bradley",
           role = c("aut", "cre"),
           email = "cobrbradley@gmail.com",
           comment = c(ORCID = "0000-0003-1616-4969")),
      person(given = "Timothy I.",
           family = "Cannings",
           role = c("aut"),
           email = "Timothy.cannings@sms.ed.ac.uk",
           comment = c(ORCID = "0000-0002-2111-4168")))
Description: Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) <arXiv:2102.04296>. This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat (>= 2.1.0)
Imports: stats, utils, glmnet, Matrix, dplyr, purrr, latex2exp,
        matrixStats, ggplot2, gglasso, PRROC
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2021-11-15 10:43:06 UTC; s1505825
Author: Jacob R. Bradley [aut, cre] (<https://orcid.org/0000-0003-1616-4969>),
  Timothy I. Cannings [aut] (<https://orcid.org/0000-0002-2111-4168>)
Maintainer: Jacob R. Bradley <cobrbradley@gmail.com>
Repository: CRAN
Date/Publication: 2021-11-15 12:00:02 UTC
Built: R 4.6.0; ; 2025-11-13 04:29:44 UTC; windows
