Package index • PERCEPTIONx

Data Loading

Download and load DepMap reference data and pre-trained models.

train_models(): Train PERCEPTIONx models for multiple drugs
get_response_matrix(): Get specific drug response data for cell-lines
get_cellLine_list(): Determine training and test cell-lines for a given drug
feature_ranking_bulk(): Feature ranking for a single drug using bulk expression
run_parallel_feature_ranking_bulk(): Parallel feature ranking for multiple drugs
build_on_BULK_v2(): Build PERCEPTIONx model on bulk expression data

annotate_clones(): Annotate cells with clone IDs via Seurat clustering
build_clone_counts(): Build clone abundance table from cell-clone mapping
build_clone_key(): Build a clone key from patient and clone id
parse_clone_keys(): Parse clone keys in "Patient@Clone" format
clone_mean_expression(): Compute clone-level mean expression from single-cell data

plot_tsne_response(): Plot UMAP with drug response overlay
plot_tsne_biomarker_viability(): Plot UMAP side-by-side for biomarker and viability
plot_clone_distribution(): Plot clone distribution as stacked bar
plot_clone_viability(): Plot clone-level viability (lollipop plot)
plot_clone_umap(): Plot UMAP colored by clone identity
plot_model_performance(): Plot model performance across datasets
plot_model_roc(): Plot validation ROC curves for trained models
plot_roc_curve(): Plot ROC curve with AUC annotation
plot_response_boxplot(): Plot predicted vs observed response boxplot
plot_seurat_clustering(): Run Seurat clustering and plot 2D embedding
plot_patient_response_panel(): Complete patient response visualization pipeline

hypergeometric_test_for_twolists(): Hypergeometric test for gene list overlap
fdrcorr(): FDR correction for multiple testing
cor.test_trimmed_v0(): Fast correlation test (generic)
export_plot_cairo(): Export plot to file via Cairo device