| barErrorPlot | Generate bar error plots | 
| barPlotCellTypes | Bar plot of deconvoluted cell type proportions | 
| blandAltmanLehPlot | Generate Bland-Altman agreement plots between predicted and expected cell type proportions of test data | 
| calculateEvalMetrics | Calculate evaluation metrics on test mixed transcriptional profiles | 
| cell.names | Get and set 'cell.names' slot in a 'PropCellTypes' object | 
| cell.names-method | Get and set 'cell.names' slot in a 'PropCellTypes' object | 
| cell.names<- | Get and set 'cell.names' slot in a 'PropCellTypes' object | 
| cell.names<--method | Get and set 'cell.names' slot in a 'PropCellTypes' object | 
| cell.types | Get and set 'cell.types' slot in a 'DeconvDLModel' object | 
| cell.types-method | Get and set 'cell.types' slot in a 'DeconvDLModel' object | 
| cell.types<- | Get and set 'cell.types' slot in a 'DeconvDLModel' object | 
| cell.types<--method | Get and set 'cell.types' slot in a 'DeconvDLModel' object | 
| corrExpPredPlot | Generate correlation plots between predicted and expected cell type proportions of test data | 
| createSpatialDDLSobject | Create a 'SpatialDDLS' object | 
| deconv.spots | Get and set 'deconv.spots' slot in a 'SpatialExperiment' object | 
| deconv.spots-method | Get and set 'deconv.spots' slot in a 'SpatialExperiment' object | 
| deconv.spots<- | Get and set 'deconv.spots' slot in a 'SpatialExperiment' object | 
| deconv.spots<--method | Get and set 'deconv.spots' slot in a 'SpatialExperiment' object | 
| DeconvDLModel | The DeconvDLModel Class | 
| DeconvDLModel-class | The DeconvDLModel Class | 
| deconvSpatialDDLS | Deconvolute spatial transcriptomics data using trained model | 
| distErrorPlot | Generate box or violin plots showing error distribution | 
| estimateZinbwaveParams | Estimate parameters of the ZINB-WaVE model to simulate new single-cell RNA-Seq expression profiles | 
| features | Get and set 'features' slot in a 'DeconvDLModel' object | 
| features-method | Get and set 'features' slot in a 'DeconvDLModel' object | 
| features<- | Get and set 'features' slot in a 'DeconvDLModel' object | 
| features<--method | Get and set 'features' slot in a 'DeconvDLModel' object | 
| genMixedCellProp | Generate training and test cell type composition matrices | 
| getProbMatrix | Getter function for the cell composition matrix | 
| installTFpython | Install Python dependencies for SpatialDDLS | 
| interGradientsDL | Calculate gradients of predicted cell types/loss function with respect to input features for interpreting trained deconvolution models | 
| loadSTProfiles | Loads spatial transcriptomics data into a SpatialDDLS object | 
| loadTrainedModelFromH5 | Load from an HDF5 file a trained deep neural network model into a 'SpatialDDLS' object | 
| method | Get and set 'method' slot in a 'PropCellTypes' object | 
| method-method | Get and set 'method' slot in a 'PropCellTypes' object | 
| method<- | Get and set 'method' slot in a 'PropCellTypes' object | 
| method<--method | Get and set 'method' slot in a 'PropCellTypes' object | 
| mixed.profiles | Get and set 'mixed.profiles' slot in a 'SpatialExperiment' object | 
| mixed.profiles-method | Get and set 'mixed.profiles' slot in a 'SpatialExperiment' object | 
| mixed.profiles<- | Get and set 'mixed.profiles' slot in a 'SpatialExperiment' object | 
| mixed.profiles<--method | Get and set 'mixed.profiles' slot in a 'SpatialExperiment' object | 
| model | Get and set 'model' slot in a 'DeconvDLModel' object | 
| model-method | Get and set 'model' slot in a 'DeconvDLModel' object | 
| model<- | Get and set 'model' slot in a 'DeconvDLModel' object | 
| model<--method | Get and set 'model' slot in a 'DeconvDLModel' object | 
| plotDistances | Plot distances between intrinsic and extrinsic profiles | 
| plotHeatmapGradsAgg | Plot a heatmap of gradients of classes / loss function wtih respect to the input | 
| plots | Get and set 'plots' slot in a 'PropCellTypes' object | 
| plots-method | Get and set 'plots' slot in a 'PropCellTypes' object | 
| plots<- | Get and set 'plots' slot in a 'PropCellTypes' object | 
| plots<--method | Get and set 'plots' slot in a 'PropCellTypes' object | 
| plotSpatialClustering | Plot results of clustering based on predicted cell proportions | 
| plotSpatialGeneExpr | Plot normalized gene expression data (logCPM) in spatial coordinates | 
| plotSpatialProp | Plot predicted proportions for a specific cell type using spatial coordinates of spots | 
| plotSpatialPropAll | Plot predicted proportions for all cell types using spatial coordinates of spots | 
| plotTrainingHistory | Plot training history of a trained SpatialDDLS deep neural network model | 
| preparingToSave | Prepare 'SpatialDDLS' object to be saved as an RDA file | 
| prob.cell.types | Get and set 'prob.cell.types' slot in a 'SpatialExperiment' object | 
| prob.cell.types-method | Get and set 'prob.cell.types' slot in a 'SpatialExperiment' object | 
| prob.cell.types<- | Get and set 'prob.cell.types' slot in a 'SpatialExperiment' object | 
| prob.cell.types<--method | Get and set 'prob.cell.types' slot in a 'SpatialExperiment' object | 
| prob.matrix | Get and set 'prob.matrix' slot in a 'PropCellTypes' object | 
| prob.matrix-method | Get and set 'prob.matrix' slot in a 'PropCellTypes' object | 
| prob.matrix<- | Get and set 'prob.matrix' slot in a 'PropCellTypes' object | 
| prob.matrix<--method | Get and set 'prob.matrix' slot in a 'PropCellTypes' object | 
| project | Get and set 'project' slot in a 'SpatialExperiment' object | 
| project-method | Get and set 'project' slot in a 'SpatialExperiment' object | 
| project<- | Get and set 'project' slot in a 'SpatialExperiment' object | 
| project<--method | Get and set 'project' slot in a 'SpatialExperiment' object | 
| PropCellTypes | The PropCellTypes Class | 
| PropCellTypes-class | The PropCellTypes Class | 
| saveRDS | Save 'SpatialExperiment' objects as RDS files | 
| saveRDS-method | Save 'SpatialExperiment' objects as RDS files | 
| saveTrainedModelAsH5 | Save a trained 'SpatialDDLS' deep neural network model to disk as an HDF5 file | 
| set | Get and set 'set' slot in a 'PropCellTypes' object | 
| set-method | Get and set 'set' slot in a 'PropCellTypes' object | 
| set.list | Get and set 'set.list' slot in a 'PropCellTypes' object | 
| set.list-method | Get and set 'set.list' slot in a 'PropCellTypes' object | 
| set.list<- | Get and set 'set.list' slot in a 'PropCellTypes' object | 
| set.list<--method | Get and set 'set.list' slot in a 'PropCellTypes' object | 
| set<- | Get and set 'set' slot in a 'PropCellTypes' object | 
| set<--method | Get and set 'set' slot in a 'PropCellTypes' object | 
| showProbPlot | Show distribution plots of the cell proportions generated by 'genMixedCellProp' | 
| simMixedProfiles | Simulate training and test mixed spot profiles | 
| simSCProfiles | Simulate new single-cell RNA-Seq expression profiles using the ZINB-WaVE model parameters | 
| single.cell.real | Get and set 'single.cell.real' slot in a 'SpatialExperiment' object | 
| single.cell.real-method | Get and set 'single.cell.real' slot in a 'SpatialExperiment' object | 
| single.cell.real<- | Get and set 'single.cell.real' slot in a 'SpatialExperiment' object | 
| single.cell.real<--method | Get and set 'single.cell.real' slot in a 'SpatialExperiment' object | 
| single.cell.simul | Get and set 'single.cell.simul' slot in a 'SpatialExperiment' object | 
| single.cell.simul-method | Get and set 'single.cell.simul' slot in a 'SpatialExperiment' object | 
| single.cell.simul<- | Get and set 'single.cell.simul' slot in a 'SpatialExperiment' object | 
| single.cell.simul<--method | Get and set 'single.cell.simul' slot in a 'SpatialExperiment' object | 
| spatial.experiments | Get and set 'spatial.experiments' slot in a 'SpatialExperiment' object | 
| spatial.experiments-method | Get and set 'spatial.experiments' slot in a 'SpatialExperiment' object | 
| spatial.experiments<- | Get and set 'spatial.experiments' slot in a 'SpatialExperiment' object | 
| spatial.experiments<--method | Get and set 'spatial.experiments' slot in a 'SpatialExperiment' object | 
| SpatialDDLS | The SpatialDDLS Class | 
| SpatialDDLS-class | The SpatialDDLS Class | 
| SpatialDDLS-Rpackage | SpatialDDLS: an R package to deconvolute spatial transcriptomics data using deep neural networks | 
| spatialPropClustering | Cluster spatial data based on predicted cell proportions | 
| test.deconv.metrics | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object | 
| test.deconv.metrics-method | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object | 
| test.deconv.metrics<- | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object | 
| test.deconv.metrics<--method | Get and set 'test.deconv.metrics' slot in a 'DeconvDLModel' object | 
| test.metrics | Get and set 'test.metrics' slot in a 'DeconvDLModel' object | 
| test.metrics-method | Get and set 'test.metrics' slot in a 'DeconvDLModel' object | 
| test.metrics<- | Get and set 'test.metrics' slot in a 'DeconvDLModel' object | 
| test.metrics<--method | Get and set 'test.metrics' slot in a 'DeconvDLModel' object | 
| test.pred | Get and set 'test.pred' slot in a 'DeconvDLModel' object | 
| test.pred-method | Get and set 'test.pred' slot in a 'DeconvDLModel' object | 
| test.pred<- | Get and set 'test.pred' slot in a 'DeconvDLModel' object | 
| test.pred<--method | Get and set 'test.pred' slot in a 'DeconvDLModel' object | 
| topGradientsCellType | Get top genes with largest/smallest gradients per cell type | 
| trainDeconvModel | Train deconvolution model for spatial transcriptomics data | 
| trained.model | Get and set 'trained.model' slot in a 'SpatialExperiment' object | 
| trained.model-method | Get and set 'trained.model' slot in a 'SpatialExperiment' object | 
| trained.model<- | Get and set 'trained.model' slot in a 'SpatialExperiment' object | 
| trained.model<--method | Get and set 'trained.model' slot in a 'SpatialExperiment' object | 
| training.history | Get and set 'training.history' slot in a 'DeconvDLModel' object | 
| training.history-method | Get and set 'training.history' slot in a 'DeconvDLModel' object | 
| training.history<- | Get and set 'training.history' slot in a 'DeconvDLModel' object | 
| training.history<--method | Get and set 'training.history' slot in a 'DeconvDLModel' object | 
| zinb.params | Get and set 'zinb.params' slot in a 'SpatialExperiment' object | 
| zinb.params-method | Get and set 'zinb.params' slot in a 'SpatialExperiment' object | 
| zinb.params<- | Get and set 'zinb.params' slot in a 'SpatialExperiment' object | 
| zinb.params<--method | Get and set 'zinb.params' slot in a 'SpatialExperiment' object | 
| ZinbParametersModel | The Class ZinbParametersModel | 
| ZinbParametersModel-class | The Class ZinbParametersModel | 
| zinbwave.model | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object | 
| zinbwave.model-method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object | 
| zinbwave.model<- | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object | 
| zinbwave.model<--method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object |