# Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization

## Documentation for package ‘dicepro’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

dicepro-package | dicepro: Semi-Supervised Deconvolution of Bulk RNA-Seq Data with Hyperparameter Optimization
best_hyperParams | Select optimal hyper-parameters using a Pareto frontier
BlueCode | BlueCode Reference Signature Matrix
CellMixtures | CellMixtures Bulk RNA-seq Dataset
contains_nan_or_inf | Check if a value contains NaN or Inf
create_gamma_lambda_plot | Visualize the gamma–lambda hyper-parameter search space
dicepro | Semi-supervised bulk RNA-seq deconvolution with hyper-parameter optimization
full_metrics | Full agreement metrics via mixed-effects modeling
generateProp | Generate Cell-Type Proportion Matrix
generate_ref_matrix | Generate a Reference Signature Matrix
heatmap_abundances | Heatmap of cell-type abundances
makeTable1Tool | Build a performance metrics table for composition matrices
metric_plot | Performance metric line plot across iterations
nmf_lbfgsb | NMF with L-BFGS-B optimization
nmf_lbfgsb_hyperOpt | NMF L-BFGS-B wrapper for hyper-parameter optimization
nrmse | Normalized Root Mean Square Error (NRMSE)
objective_opt | Objective function for hyper-parameter optimization
plot.dicepro | Plot cell abundance heatmap and error plot
plot_hyperopt | Plot hyperparameter optimization report
plot_hyperopt.dicepro | Plot hyperparameter optimization report
research_hyperOpt | Hyper-parameter optimization loop for dicepro
row_norm_pos | Row-normalize a matrix with non-negative clamping
running_method | Run cell-type deconvolution
run_CSx | Run CIBERSORTx Deconvolution Method
run_experiment | Run a dicepro hyperparameter optimization experiment
samplewise_metrics | Sample-wise Pearson correlation and RMSE
simulation | Simulate Bulk RNA-seq Data with Biological and Technical Noise
simulation_bluecode | Simulate Bulk RNA-seq Data Using the BlueCode Reference Matrix