Package: dicepro
Title: Semi-Supervised Deconvolution of Bulk RNA-Seq Data with
        Hyperparameter Optimization
Version: 1.0.2
Authors@R: c(
    person("Kalidou", "BA",
           role  = c("aut", "cre"),
           email = "sistm.soft.maintain@gmail.com"),
    person("Boris P.", "Hejblum",
           role  = "aut",
           email = "boris.hejblum@u-bordeaux.fr"))
Description: Performs semi-supervised deconvolution of bulk RNA sequencing
    (RNA-seq) data. Known cell-type proportions are estimated using
    supervised methods -- 'CIBERSORTx' (CSx), 'CIBERSORT' (CS), 'FARDEEP' (Fast
    And Robust DEconvolution of Expression Profiles), and 'DCQ' (Digital
    Cell Quantifier) -- while unknown components are inferred using
    non-negative matrix factorization ('NMF') with limited-memory
    Broyden-Fletcher-Goldfarb-Shanno with bounds ('L-BFGS-B') optimization.
    Hyperparameters are selected automatically using a Pareto-frontier-based
    approach with knee-point detection, allowing application when the
    reference signature matrix is incomplete. More details about 'DICEpro' can 
    be found in Ba et al. (2026) <doi:10.64898/2026.06.17.732876>.
Depends: R (>= 4.1.0)
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: true
LazyDataCompression: xz
Config/testthat/edition: 3
VignetteBuilder: knitr
LinkingTo: Rcpp (>= 1.0.12), RcppEigen
Imports: Rcpp (>= 1.0.12), lbfgsb3c, KraljicMatrix, ggplot2, patchwork,
        FARDEEP, ComICS, lme4, e1071, preprocessCore, parallel
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/kalidouBA/dicepro
BugReports: https://github.com/kalidouBA/dicepro/issues
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2026-06-24 10:46:56 UTC; kalidou
Author: Kalidou BA [aut, cre],
  Boris P. Hejblum [aut]
Maintainer: Kalidou BA <sistm.soft.maintain@gmail.com>
Repository: CRAN
Date/Publication: 2026-06-30 12:20:14 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-08-17 03:56:34 UTC; windows
Archs: x64
