# comparative single-cell transcriptomics between disease models and a human condition

## Documentation for package ‘singIST’ version 1.1.0

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

## Help Pages

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
calculate_pvalues | Update block of predictor matrices in matrixToBlock()
celltype_mapping | Cell type mapping
celltype_recap | Derive cell type recapitulation
center_scale | Update block of predictor matrices in matrixToBlock()
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
CIP_GIP | Compute Cell Importance Projection (CIP) and Gene Importance Projection (GIP)
CIP_GIP_test | Cell and Gene Importance Projections statistical significance
clean_mfa_data | Clean a predictor matrix for multiblock MFA
compute_final_measures | Update block of predictor matrices in matrixToBlock()
compute_IC95 | Update block of predictor matrices in matrixToBlock()
compute_permutation_stats | Update block of predictor matrices in matrixToBlock()
compute_pvalue | Update block of predictor matrices in matrixToBlock()
compute_validation_metrics | Update block of predictor matrices in matrixToBlock()
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
deflate_prediction | Update block of predictor matrices in matrixToBlock()
derive_contributions | Derive superpathway score, cell type contribution and gene contribution
derive_scores | Compute predictor scores
detect_gene_type | Update block of predictor matrices in matrixToBlock()
diff_expressed | Compute differentially expressed genes with FindMarkers/findMarkers and descriptive point estimates of log2FC
evaluate_performance | Update block of predictor matrices in matrixToBlock()
evaluate_quantile_combinations | Update block of predictor matrices in matrixToBlock()
execute_parallel_cv | Update block of predictor matrices in matrixToBlock()
execute_sequential_cv | Update block of predictor matrices in matrixToBlock()
FCtoExpression | Update block of predictor matrices in matrixToBlock()
fitOptimal | Cross validation and fit of asmbPLSDA
fit_mfa_imputer | Fit a multiblock‐MFA imputer on training data
fit_permuted_model | Update block of predictor matrices in matrixToBlock()
generate_null_distributions | Update block of predictor matrices in matrixToBlock()
gene_contrib | Derive gene contribution to cell type recapitulation
get_indices | Update block of predictor matrices in matrixToBlock()
get_measure_index | Update block of predictor matrices in matrixToBlock()
get_train_val_sets | Update block of predictor matrices in matrixToBlock()
helpers | Update block of predictor matrices in matrixToBlock()
initialize_results | Update block of predictor matrices in matrixToBlock()
jackknife_CIP_GIP | 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
performance_measures | Update block of predictor matrices in matrixToBlock()
perform_cv | Update block of predictor matrices in matrixToBlock()
permute_X_matrix | Update block of predictor matrices in matrixToBlock()
permute_Y_matrix | Update block of predictor matrices in matrixToBlock()
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
quantile_computation | Update block of predictor matrices in matrixToBlock()
render_multiple_outputs | Render multiple singISTrecapitulation outputs
restore_removed_columns | Restore columns removed during MFA cleaning into the imputed matrix
Results_comparison_measure | Compute performance metrics of predicted asmbPLSDA
retrieve_one2one_orthologs | Update block of predictor matrices in matrixToBlock()
select_optimal_PLS | Update block of predictor matrices in matrixToBlock()
select_samples | Update block of predictor matrices in matrixToBlock()
setGeneSetsCelltype | Set gene sets per cell type in a superpathway
singISTrecapitulations | Compute singIST recapitulations
singIST_treat | Derive singIST treated samples
subsampling_CIP_GIP | Update block of predictor matrices in matrixToBlock()
superpathway_recap | Derive superpathway recapitulation
update_block | Update block of predictor matrices in matrixToBlock()
update_group_sizes | Update block‐size vector after cleaning
wilcox_CIP_GIP | Mann-Whitney Wilcoxon test p-value