BlueCode                BlueCode Reference Signature Matrix
CellMixtures            CellMixtures Bulk RNA-seq Dataset
best_hyperParams        Select optimal hyper-parameters using a Pareto
                        frontier
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
dicepro-package         dicepro: Semi-Supervised Deconvolution of Bulk
                        RNA-Seq Data with Hyperparameter 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
research_hyperOpt       Hyper-parameter optimization loop for dicepro
row_norm_pos            Row-normalize a matrix with non-negative
                        clamping
run_CSx                 Run CIBERSORTx Deconvolution Method
run_experiment          Run a dicepro hyperparameter optimization
                        experiment
running_method          Run cell-type deconvolution
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
