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) . 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: 2026-06-30 16:50:23 UTC; root Author: Kalidou BA [aut, cre], Boris P. Hejblum [aut] Maintainer: Kalidou BA Repository: https://cran.r-universe.dev Date/Publication: 2026-06-30 12:20:14 UTC RemoteUrl: https://github.com/cran/dicepro RemoteRef: HEAD RemoteSha: 98e5ba8f5f2b183b41c6e8ac541ab2773c0f5733