DigitalDLSorter-class   The DigitalDLSorter Class
DigitalDLSorterDNN-class
                        The DigitalDLSorterDNN Class
ProbMatrixCellTypes-class
                        The Class ProbMatrixCellTypes
ZinbParametersModel-class
                        The Class ZinbParametersModel
barErrorPlot            Generate bar error plots
barPlotCellTypes        Bar plot of deconvoluted cell type proportions
                        in bulk RNA-Seq samples
blandAltmanLehPlot      Generate Bland-Altman agreement plots between
                        predicted and expected cell type proportions
                        from test data results
bulk.simul              Get and set 'bulk.simul' slot in a
                        'DigitalDLSorter' object
calculateEvalMetrics    Calculate evaluation metrics for bulk RNA-Seq
                        samples from test data
cell.names              Get and set 'cell.names' slot in a
                        'ProbMatrixCellTypes' object
cell.types              Get and set 'cell.types' slot in a
                        'DigitalDLSorterDNN' object
corrExpPredPlot         Generate correlation plots between predicted
                        and expected cell type proportions from test
                        data
deconv.data             Get and set 'deconv.data' slot in a
                        'DigitalDLSorter' object
deconv.results          Get and set 'deconv.results' slot in a
                        'DigitalDLSorter' object
deconvDigitalDLSorter   Deconvolute bulk RNA-Seq samples using a
                        pre-trained DigitalDLSorter model
deconvDigitalDLSorterObj
                        Deconvolute bulk gene expression samples (bulk
                        RNA-Seq)
digitalDLSorteR         digitalDLSorteR: an R package to deconvolute
                        bulk RNA-Seq samples using single-cell RNA-Seq
                        data and Deep Learning
distErrorPlot           Generate box plots or violin plots to show how
                        the errors are distributed
estimateZinbwaveParams
                        Estimate the parameters of the ZINB-WaVE model
                        to simulate new single-cell RNA-Seq expression
                        profiles
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
listToDDLS              Transform DigitalDLSorter-like list into an
                        actual DigitalDLSorterDNN object
listToDDLSDNN           Transform DigitalDLSorterDNN-like list into an
                        actual DigitalDLSorterDNN object
loadDeconvData          Load data to be deconvoluted into a
                        DigitalDLSorter object
loadSCProfiles          Create a 'DigitalDLSorter' object from
                        single-cell RNA-seq data
loadTrainedModelFromH5
                        Load from an HDF5 file a trained Deep Neural
                        Network model into a 'DigitalDLSorter' object
method                  Get and set 'method' slot in a
                        'ProbMatrixCellTypes' object
model                   Get and set 'model' slot in a
                        'DigitalDLSorterDNN' object
plotTrainingHistory     Plot training history of a trained
                        DigitalDLSorter Deep Neural Network model
plots                   Get and set 'plots' slot in a
                        'ProbMatrixCellTypes' object
preparingToSave         Prepare 'DigitalDLSorter' object to be saved as
                        an RDA file
prob.cell.types         Get and set 'prob.cell.types' slot in a
                        'DigitalDLSorter' object
prob.matrix             Get and set 'prob.matrix' slot in a
                        'ProbMatrixCellTypes' object
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 disk as an HDF5 file
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 'generateBulkCellMatrix'
simBulkProfiles         Simulate training and test pseudo-bulk RNA-Seq
                        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
                        'DigitalDLSorter' object
single.cell.simul       Get and set 'single.cell.simul' slot in a
                        'DigitalDLSorter' object
test.deconv.metrics     Get and set 'test.deconv.metrics' slot in a
                        'DigitalDLSorterDNN' object
test.metrics            Get and set 'test.metrics' slot in a
                        'DigitalDLSorterDNN' object
test.pred               Get and set 'test.pred' slot in a
                        'DigitalDLSorterDNN' object
trainDigitalDLSorterModel
                        Train Deep Neural Network model
trained.model           Get and set 'trained.model' slot in a
                        'DigitalDLSorter' object
training.history        Get and set 'training.history' slot in a
                        'DigitalDLSorterDNN' object
zinb.params             Get and set 'zinb.params' slot in a
                        'DigitalDLSorter' object
zinbwave.model          Get and set 'zinbwave.model' slot in a
                        'ZinbParametersModel' object
