SpatialDDLS
Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Package index
Search the SpatialDDLS package
Vignettes
Functions
259
Source code
21
Man pages
60
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SpatialDDLS: Deconvolution of Spatial Transcriptomics Data Based on Neural Networks
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API

API for SpatialDDLS
Deconvolution of Spatial Transcriptomics Data Based on Neural Networks

Global functions
.AbsErr Source code
.SqrErr Source code
.aggregate.Matrix.cast Source code
.aggregate.Matrix.sparse 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
.distCalc Source code
.downsampleCells Source code
.extractDataFromSE Source code
.filterGenesByCells Source code
.filterGenesByCluster Source code
.filterGenesHDF5 Source code
.filterGenesSparse Source code
.finalShow Source code
.generateBulkProfiles Source code
.generateExcludedTypes Source code
.generateExcludedTypesScaled Source code
.generateSetDir Source code
.generateSetPure Source code
.isConda Source code
.isPython Source code
.isTensorFlow Source code
.labelsCCCFacet Source code
.labelsErrorFacet Source code
.linesPlot Source code
.loadModelFromJSON Source code
.loadSCData Source code
.loadSTData 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
.processData Source code
.processSTData Source code
.randomStr 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
.spatialRegularization 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
DeconvDLModel Man page
DeconvDLModel-class Man page
PropCellTypes Man page
PropCellTypes-class Man page
SpatialDDLS Man page
SpatialDDLS-Rpackage Man page
SpatialDDLS-class Man page
SpatialDDLS-package Man page
SpatialDDLSTheme Source code
ZinbParametersModel Man page
ZinbParametersModel-class Man page
aggregation.fun.add.cpm Source code
aggregation.fun.add.raw.counts Source code
aggregation.fun.add.raw.counts.cpm Source code
aggregation.fun.mean.cpm Source code
barErrorPlot Man page Source code
barPlotCellTypes Man page Source code
blandAltmanLehPlot Man page Source code
calculateEvalMetrics Man page Source code
cell.names Man page
cell.names,PropCellTypes-method Man page
cell.names<- Man page
cell.names<-,PropCellTypes-method Man page
cell.types Man page
cell.types,DeconvDLModel-method Man page
cell.types<- Man page
cell.types<-,DeconvDLModel-method Man page
corrExpPredPlot Man page Source code
createSpatialDDLSobject Man page Source code
deconv.spots Man page
deconv.spots,SpatialDDLS-method Man page
deconv.spots<- Man page
deconv.spots<-,SpatialDDLS-method Man page
deconvSpatialDDLS Man page Source code
default.colors Source code
distErrorPlot Man page Source code
estimateZinbwaveParams Man page Source code
features Man page
features,DeconvDLModel-method Man page
features<- Man page
features<-,DeconvDLModel-method Man page
genMixedCellProp Man page Source code
getProbMatrix Man page Source code
installTFpython Man page Source code
interGradientsDL Man page Source code
loadSTProfiles Man page Source code
loadTrainedModelFromH5 Man page Source code
method Man page
method,PropCellTypes-method Man page
method<- Man page
method<-,PropCellTypes-method Man page
mixed.profiles Man page
mixed.profiles,SpatialDDLS-method Man page
mixed.profiles<- Man page
mixed.profiles<-,SpatialDDLS-method Man page
model Man page
model,DeconvDLModel-method Man page
model<- Man page
model<-,DeconvDLModel-method Man page
plotDistances Man page Source code
plotHeatmapGradsAgg Man page Source code
plotSpatialClustering Man page Source code
plotSpatialGeneExpr Man page Source code
plotSpatialProp Man page Source code
plotSpatialPropAll Man page Source code
plotTrainingHistory Man page Source code
plots Man page
plots,PropCellTypes-method Man page
plots<- Man page
plots<-,PropCellTypes-method Man page
preparingToSave Man page Source code
prob.cell.types Man page
prob.cell.types,SpatialDDLS-method Man page
prob.cell.types<- Man page
prob.cell.types<-,SpatialDDLS-method Man page
prob.matrix Man page
prob.matrix,PropCellTypes-method Man page
prob.matrix<- Man page
prob.matrix<-,PropCellTypes-method Man page
project Man page
project,SpatialDDLS-method Man page
project<- Man page
project<-,SpatialDDLS-method Man page
rescale.function Source code
rescale.function.2 Source code
saveRDS Man page
saveRDS,DeconvDLModel-method Man page
saveRDS,SpatialDDLS-method Man page
saveRDS,saveRDS-method Man page
saveTrainedModelAsH5 Man page Source code
se Source code
set Man page
set,PropCellTypes-method Man page
set.list Man page
set.list,PropCellTypes-method Man page
set.list<- Man page
set.list<-,PropCellTypes-method Man page
set<- Man page
set<-,PropCellTypes-method Man page
setCount Source code
showProbPlot Man page Source code
simMixedProfiles Man page Source code
simSCProfiles Man page Source code
single.cell.real Man page
single.cell.real,SpatialDDLS-method Man page
single.cell.real<- Man page
single.cell.real<-,SpatialDDLS-method Man page
single.cell.simul Man page
single.cell.simul,SpatialDDLS-method Man page
single.cell.simul<- Man page
single.cell.simul<-,SpatialDDLS-method Man page
spatial.experiments Man page
spatial.experiments,SpatialDDLS-method Man page
spatial.experiments<- Man page
spatial.experiments<-,SpatialDDLS-method Man page
spatialPropClustering Man page Source code
test.deconv.metrics Man page
test.deconv.metrics,DeconvDLModel-method Man page
test.deconv.metrics<- Man page
test.deconv.metrics<-,DeconvDLModel-method Man page
test.metrics Man page
test.metrics,DeconvDLModel-method Man page
test.metrics<- Man page
test.metrics<-,DeconvDLModel-method Man page
test.pred Man page
test.pred,DeconvDLModel-method Man page
test.pred<- Man page
test.pred<-,DeconvDLModel-method Man page
top.gradients Source code
topGradientsCellType Man page Source code
trainDeconvModel Man page Source code
trained.model Man page
trained.model,SpatialDDLS-method Man page
trained.model<- Man page
trained.model<-,SpatialDDLS-method Man page
training.history Man page
training.history,DeconvDLModel-method Man page
training.history<- Man page
training.history<-,DeconvDLModel-method Man page
zinb.params Man page
zinb.params,SpatialDDLS-method Man page
zinb.params<- Man page
zinb.params<-,SpatialDDLS-method Man page
zinbwave.model Man page
zinbwave.model,ZinbParametersModel-method Man page
zinbwave.model<- Man page
zinbwave.model<-,ZinbParametersModel-method Man page
SpatialDDLS documentation built on Oct. 31, 2024, 5:07 p.m.

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