Man pages for digitalDLSorteR
Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
| barErrorPlot | Generate bar error plots |
| barPlotCellTypes | Bar plot of deconvoluted cell type proportions in bulk... |
| blandAltmanLehPlot | Generate Bland-Altman agreement plots between predicted and... |
| bulk.simul | Get and set 'bulk.simul' slot in a 'DigitalDLSorter' object |
| calculateEvalMetrics | Calculate evaluation metrics for bulk RNA-Seq samples from... |
| cell.names | Get and set 'cell.names' slot in a 'ProbMatrixCellTypes'... |
| cell.types | Get and set 'cell.types' slot in a 'DigitalDLSorterDNN'... |
| corrExpPredPlot | Generate correlation plots between predicted and expected... |
| createDDLSobject | Create a 'DigitalDLSorter' object from single-cell RNA-seq... |
| deconv.data | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
| deconvDDLSObj | Deconvolute bulk gene expression samples (bulk RNA-Seq) |
| deconvDDLSPretrained | Deconvolute bulk RNA-Seq samples using a pre-trained... |
| deconv.results | Get and set 'deconv.results' slot in a 'DigitalDLSorter'... |
| digitalDLSorteR | digitalDLSorteR: an R package to deconvolute bulk RNA-Seq... |
| DigitalDLSorter-class | The DigitalDLSorter Class |
| DigitalDLSorterDNN-class | The DigitalDLSorterDNN Class |
| distErrorPlot | Generate box plots or violin plots to show how the errors are... |
| estimateZinbwaveParams | Estimate the parameters of the ZINB-WaVE model to simulate... |
| features | Get and set 'features' slot in a 'DigitalDLSorterDNN' object |
| generateBulkCellMatrix | Generate training and test cell composition matrices |
| getProbMatrix | Getter function for the cell composition matrix |
| installTFpython | Install Python dependencies for digitalDLSorteR |
| interGradientsDL | Calculate gradients of predicted cell types/loss function... |
| listToDDLS | Transform DigitalDLSorter-like list into an actual... |
| listToDDLSDNN | Transform DigitalDLSorterDNN-like list into an actual... |
| loadDeconvData | Load data to be deconvoluted into a DigitalDLSorter object |
| loadTrainedModelFromH5 | Load from an HDF5 file a trained Deep Neural Network model... |
| method | Get and set 'method' slot in a 'ProbMatrixCellTypes' object |
| model | Get and set 'model' slot in a 'DigitalDLSorterDNN' object |
| plotHeatmapGradsAgg | Plot a heatmap of gradients of classes / loss function wtih... |
| plots | Get and set 'plots' slot in a 'ProbMatrixCellTypes' object |
| plotTrainingHistory | Plot training history of a trained DigitalDLSorter Deep... |
| preparingToSave | Prepare 'DigitalDLSorter' object to be saved as an RDA file |
| prob.cell.types | Get and set 'prob.cell.types' slot in a 'DigitalDLSorter'... |
| prob.matrix | Get and set 'prob.matrix' slot in a 'ProbMatrixCellTypes'... |
| ProbMatrixCellTypes-class | The Class ProbMatrixCellTypes |
| project | Get and set 'project' slot in a 'DigitalDLSorter' object |
| saveRDS | Save 'DigitalDLSorter' objects as RDS files |
| saveTrainedModelAsH5 | Save a trained 'DigitalDLSorter' Deep Neural Network model to... |
| set | Get and set 'set' slot in a 'ProbMatrixCellTypes' object |
| set.list | Get and set 'set.list' slot in a 'ProbMatrixCellTypes' object |
| showProbPlot | Show distribution plots of the cell proportions generated by... |
| simBulkProfiles | Simulate training and test pseudo-bulk RNA-Seq profiles |
| simSCProfiles | Simulate new single-cell RNA-Seq expression profiles using... |
| single.cell.real | Get and set 'single.cell.real' slot in a 'DigitalDLSorter'... |
| single.cell.simul | Get and set 'single.cell.simul' slot in a 'DigitalDLSorter'... |
| test.deconv.metrics | Get and set 'test.deconv.metrics' slot in a... |
| test.metrics | Get and set 'test.metrics' slot in a 'DigitalDLSorterDNN'... |
| test.pred | Get and set 'test.pred' slot in a 'DigitalDLSorterDNN' object |
| topGradientsCellType | Get top genes with largest/smallest gradients per cell type |
| trainDDLSModel | Train Deep Neural Network model |
| trained.model | Get and set 'trained.model' slot in a 'DigitalDLSorter'... |
| training.history | Get and set 'training.history' slot in a 'DigitalDLSorterDNN'... |
| ZinbParametersModel-class | The Class ZinbParametersModel |
| zinb.params | Get and set 'zinb.params' slot in a 'DigitalDLSorter' object |
| zinbwave.model | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel'... |
