GenerateInput           Generate pattern level data for cell type
                        annotation
GenerateReference       Generate reference pattern labels (no default
                        writing)
Input_training          Train XGBoost model to predict cell type
Liu2021_MouseBrain_P1000
                        Load the Liu et al. mouse brain pretrained
                        model
PlotConfusion           Generate confusion table for the final
                        prediction
PlotF1                  Generate F1 score barplot for each class
PlotUMAP                Generate UMAP for the final prediction based on
                        cell patterns
PlotUMAP_fixedwindow    Generate UMAP for the final prediction based on
                        fixed window eg.100kb bin widows
PredictCellType         Predict cell type annotation from the trained
                        model
Zhou2025_HumanAtlas_P1000
                        Load the Zhou et al. human atlas pretrained
                        model
confidence_score        Produce confidence score for XGBoost prediction
confidence_score_top95
                        Produce confidence score based on top 95
                        percent for XGBoost prediction
filter_cell             Filter final prediction to reduce noise
imputeRowMean           Impute missing value for 100K window matrix
nnls_deconv             Estimate cell type relative proportion
smooth_matrix           Smooth cell by pattern matrix to reduce noise
