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>.
| Version: | 1.0.2 |
| Depends: | R (≥ 4.1.0) |
| Imports: | Rcpp (≥ 1.0.12), lbfgsb3c, KraljicMatrix, ggplot2, patchwork, FARDEEP, ComICS, lme4, e1071, preprocessCore, parallel |
| LinkingTo: | Rcpp (≥ 1.0.12), RcppEigen |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| Published: | 2026-06-30 |
| DOI: | 10.32614/CRAN.package.dicepro (may not be active yet) |
| Author: | Kalidou BA [aut, cre], Boris P. Hejblum [aut] |
| Maintainer: | Kalidou BA <sistm.soft.maintain at gmail.com> |
| BugReports: | https://github.com/kalidouBA/dicepro/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/kalidouBA/dicepro |
| NeedsCompilation: | yes |
| Materials: | README, NEWS |
| CRAN checks: | dicepro results |
| Reference manual: | dicepro.html , dicepro.pdf |
| Vignettes: |
dicepro - Hyperparameter Search Space Visualization (source, R code) dicepro - Real Data Workflow (BlueCode + CellMixtures) (source, R code) dicepro - Simulated Data Workflow (source, R code) |
| Package source: | dicepro_1.0.2.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): dicepro_1.0.2.tgz, r-oldrel (x86_64): not available |
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