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dicepro  

Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization
View on CRAN: Click here


Download and install dicepro package within the R console
Install from CRAN:
install.packages("dicepro")

Install from Github:
library("remotes")
install_github("cran/dicepro")

Install by package version:
library("remotes")
install_version("dicepro", "1.0.2")



Attach the package and use:
library("dicepro")
Maintained by
Kalidou BA
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2026-06-30
Latest Update: 2026-06-30
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>.
How to cite:
Kalidou BA (2026). dicepro: Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization. R package version 1.0.2, https://cran.r-project.org/web/packages/dicepro. Accessed 24 Oct. 2026.
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