digitalDLSorteR
Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

Package index
Search the digitalDLSorteR package
Vignettes
Functions
254
Source code
19
Man pages
56
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digitalDLSorteR: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
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API

API for digitalDLSorteR
Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

Global functions
.AbsErr Source code
.SqrErr Source code
.adjustHundred Source code
.allSlotsNull Source code
.barPlot Source code
.boxPlot Source code
.bulkShow Source code
.calcGradientsClass Source code
.calcGradientsLoss Source code
.calculateMetrics Source code
.cccCalculation Source code
.cellExcluder Source code
.checkColumn Source code
.checkHDF5parameters Source code
.checkNumCellTypes Source code
.checkPythonDependencies Source code
.checkSlot Source code
.cpmCalculate Source code
.createSCEObject Source code
.createSEObject Source code
.dataForDNN.file Source code
.dataForDNN.onFly Source code
.deconvCore Source code
.extractDataFromSCE Source code
.extractDataFromSE Source code
.filterGenesByCells Source code
.filterGenesByCluster Source code
.filterGenesByVar Source code
.filterGenesHDF5 Source code
.filterGenesSparse Source code
.finalShow Source code
.generateBulkProfiles Source code
.generateExcludedTypes Source code
.generateSet1 Source code
.generateSet2 Source code
.generateSet3 Source code
.generateSet4 Source code
.generateSet5 Source code
.generateSet6 Source code
.isConda Source code
.isPython Source code
.isTensorFlow Source code
.labelsCCCFacet Source code
.labelsErrorFacet Source code
.linesPlot Source code
.loadBulkData Source code
.loadModelFromJSON Source code
.loadSCData Source code
.logicalFiltSparse Source code
.meanErr Source code
.mergeMatrices Source code
.mergePropsSort Source code
.onLoad Source code
.plotsQCSets Source code
.ppAbsErr Source code
.ppSqrErr Source code
.predictDeconvDataGenerator Source code
.predictGenerator Source code
.processBulkData Source code
.processData Source code
.randomStr Source code Source code
.readCountsFile Source code
.readTabFiles Source code
.reduceDataset Source code
.saveModelToJSON Source code
.sceShow Source code
.sel.genes.sign Source code
.selectSome Source code
.setBulk Source code
.setHundredLimit Source code
.simplifyMajority Source code
.simplifyMajorityGeneral Source code
.simplifySet Source code
.simplifySetGeneral Source code
.statsBlock Source code
.subsetCells Source code
.targetForDNN Source code
.trainGenerator Source code
.updateAMD Source code
.useH5backend Source code
.violinPlot Source code
.zinbModelShow Source code
.zinbWaveModel Source code
DigitalDLSorter Man page
DigitalDLSorter-class Man page
DigitalDLSorterDNN Man page
DigitalDLSorterDNN-class Man page
DigitalDLSorterTheme Source code
ProbMatrixCellTypes Man page
ProbMatrixCellTypes-class Man page
ZinbParametersModel Man page
ZinbParametersModel-class Man page
barErrorPlot Man page Source code
barPlotCellTypes Man page
barPlotCellTypes,ANY-method Man page
barPlotCellTypes,DigitalDLSorter-method Man page
blandAltmanLehPlot Man page Source code
bulk.simul Man page
bulk.simul,DigitalDLSorter-method Man page
bulk.simul<- Man page
bulk.simul<-,DigitalDLSorter-method Man page
calculateEvalMetrics Man page Source code
cell.names Man page
cell.names,ProbMatrixCellTypes-method Man page
cell.names<- Man page
cell.names<-,ProbMatrixCellTypes-method Man page
cell.types Man page
cell.types,DigitalDLSorterDNN-method Man page
cell.types<- Man page
cell.types<-,DigitalDLSorterDNN-method Man page
corrExpPredPlot Man page Source code
createDDLSobject Man page Source code
deconv.data Man page
deconv.data,DigitalDLSorter-method Man page
deconv.data<- Man page
deconv.data<-,DigitalDLSorter-method Man page
deconv.results Man page
deconv.results,DigitalDLSorter-method Man page
deconv.results<- Man page
deconv.results<-,DigitalDLSorter-method Man page
deconvDDLSObj Man page Source code
deconvDDLSPretrained Man page Source code
default.colors Source code
digitalDLSorteR Man page
distErrorPlot Man page Source code
estimateZinbwaveParams Man page Source code
features Man page
features,DigitalDLSorterDNN-method Man page
features<- Man page
features<-,DigitalDLSorterDNN-method Man page
generateBulkCellMatrix Man page Source code
getProbMatrix Man page Source code
installTFpython Man page
interGradientsDL Man page Source code
listToDDLS Man page Source code
listToDDLSDNN Man page Source code
loadDeconvData Man page
loadDeconvData,DigitalDLSorter,SummarizedExperiment-method Man page
loadDeconvData,DigitalDLSorter,character-method Man page
loadTrainedModelFromH5 Man page Source code
method Man page
method,ProbMatrixCellTypes-method Man page
method<- Man page
method<-,ProbMatrixCellTypes-method Man page
model Man page
model,DigitalDLSorterDNN-method Man page
model<- Man page
model<-,DigitalDLSorterDNN-method Man page
plotHeatmapGradsAgg Man page Source code
plotTrainingHistory Man page Source code
plots Man page
plots,ProbMatrixCellTypes-method Man page
plots<- Man page
plots<-,ProbMatrixCellTypes-method Man page
preparingToSave Man page Source code
prob.cell.types Man page
prob.cell.types,DigitalDLSorter-method Man page
prob.cell.types<- Man page
prob.cell.types<-,DigitalDLSorter-method Man page
prob.matrix Man page
prob.matrix,ProbMatrixCellTypes-method Man page
prob.matrix<- Man page
prob.matrix<-,ProbMatrixCellTypes-method Man page
project Man page
project,DigitalDLSorter-method Man page
project<- Man page
project<-,DigitalDLSorter-method Man page
pseudobulk.fun.add.cpm Source code
pseudobulk.fun.add.raw.counts Source code
pseudobulk.fun.add.raw.counts.cpm Source code
pseudobulk.fun.mean.cpm Source code
rescale.function Source code
saveRDS Man page
saveRDS,DigitalDLSorter-method Man page
saveRDS,DigitalDLSorterDNN-method Man page
saveRDS,saveRDS-method Man page
saveTrainedModelAsH5 Man page Source code
se Source code
set Man page
set,ProbMatrixCellTypes-method Man page
set.list Man page
set.list,ProbMatrixCellTypes-method Man page
set.list<- Man page
set.list<-,ProbMatrixCellTypes-method Man page
set<- Man page
set<-,ProbMatrixCellTypes-method Man page
setCount Source code
showProbPlot Man page Source code
simBulkProfiles Man page Source code
simSCProfiles Man page Source code
single.cell.real Man page
single.cell.real,DigitalDLSorter-method Man page
single.cell.real<- Man page
single.cell.real<-,DigitalDLSorter-method Man page
single.cell.simul Man page
single.cell.simul,DigitalDLSorter-method Man page
single.cell.simul<- Man page
single.cell.simul<-,DigitalDLSorter-method Man page
test.deconv.metrics Man page
test.deconv.metrics,DigitalDLSorterDNN-method Man page
test.deconv.metrics<- Man page
test.deconv.metrics<-,DigitalDLSorterDNN-method Man page
test.metrics Man page
test.metrics,DigitalDLSorterDNN-method Man page
test.metrics<- Man page
test.metrics<-,DigitalDLSorterDNN-method Man page
test.pred Man page
test.pred,DigitalDLSorterDNN-method Man page
test.pred<- Man page
test.pred<-,DigitalDLSorterDNN-method Man page
top.gradients Source code
topGradientsCellType Man page Source code
trainDDLSModel Man page Source code
trained.model Man page
trained.model,DigitalDLSorter-method Man page
trained.model<- Man page
trained.model<-,DigitalDLSorter-method Man page
training.history Man page
training.history,DigitalDLSorterDNN-method Man page
training.history<- Man page
training.history<-,DigitalDLSorterDNN-method Man page
zinb.params Man page
zinb.params,DigitalDLSorter-method Man page
zinb.params<- Man page
zinb.params<-,DigitalDLSorter-method Man page
zinbwave.model Man page
zinbwave.model,ZinbParametersModel-method Man page
zinbwave.model<- Man page
zinbwave.model<-,ZinbParametersModel-method Man page
digitalDLSorteR documentation built on Sept. 13, 2024, 5:06 p.m.

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