CIP_GIP                 Compute Cell Importance Projection (CIP) and
                        Gene Importance Projection (GIP)
CIP_GIP_test            Cell and Gene Importance Projections
                        statistical significance
Results_comparison_measure
                        Compute performance metrics of predicted
                        asmbPLSDA
add_missing_psb_rows    Ensure all celltype–sample combinations are
                        present in the pseudobulkmatrix
asmbPLSDA.cv.kcv        K‐fold × Repeated Cross‐Validation for
                        asmbPLS-DA
asmbPLSDA.cv.loo        Leave-one-out Cross-validation
biological_link_function
                        Biological link function
celltype_mapping        Cell type mapping
celltype_recap          Derive cell type recapitulation
check_fit_model         Validate superpathway fit model
check_hyperparameters   Validate asmbPLS-DA hyperparameters
check_mapping_organism
                        Validate mapping organism input
check_pathway           Validate pathway fields
check_superpathway      Validate superpathway gene sets
check_superpathway_input
                        Check superpathway input for asmbPLS-DA
clean_mfa_data          Clean a predictor matrix for multiblock MFA
create_fit_model        Create superpathway fit model object
create_hyperparameters
                        Create asmbPLS-DA hyperparameters object
create_mapping_organism
                        Create mapping organism object
create_pathway          Create pathway object
create_superpathway     Create superpathway gene sets object
create_superpathway_input
                        Create superpathway input for asmbPLS-DA
derive_contributions    Derive superpathway score, cell type
                        contribution and gene contribution
derive_scores           Compute predictor scores
diff_expressed          Compute differentially expressed genes with
                        FindMarkers/findMarkers and descriptive point
                        estimates of log2FC
fitOptimal              Cross validation and fit of asmbPLSDA
fit_mfa_imputer         Fit a multiblock‐MFA imputer on training data
gene_contrib            Derive gene contribution to cell type
                        recapitulation
helpers                 Update block of predictor matrices in
                        matrixToBlock()
matrixToBlock           Build predictor and response blocks with
                        superpathway input
multiple_check          Check if parameter format is consistent
multiple_fitOptimal     Multiple Cross validation and fit of asmbPLSDA
multiple_singISTrecapitulations
                        Compute singIST recapitulations for multiple
                        superpathways
orthology_mapping       Orthology mapping
permut_asmbplsda        Permutation test for asmbPLSDA global
                        significance for LOO
permut_asmbplsda_kcv    Permutation test for asmbPLS-DA global
                        significance (LOO or KCV)
predict_mfa_imputer     Impute new samples using a fitted MFA imputer
pullGeneSet             Pull Gene Set from MsigDB
render_multiple_outputs
                        Render multiple singISTrecapitulation outputs
restore_removed_columns
                        Restore columns removed during MFA cleaning
                        into the imputed matrix
setGeneSetsCelltype     Set gene sets per cell type in a superpathway
singIST_treat           Derive singIST treated samples
singISTrecapitulations
                        Compute singIST recapitulations
superpathway_recap      Derive superpathway recapitulation
update_group_sizes      Update block‐size vector after cleaning
wilcox_CIP_GIP          Mann-Whitney Wilcoxon test p-value
