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... |
deconv.data | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
deconvDigitalDLSorter | Deconvolute bulk RNA-Seq samples using a pre-trained... |
deconvDigitalDLSorterObj | Deconvolute bulk gene expression samples (bulk RNA-Seq) |
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 |
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 |
loadSCProfiles | Create a 'DigitalDLSorter' object from single-cell RNA-seq... |
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 |
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 |
trainDigitalDLSorterModel | 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'... |
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