DigitalCellSorter
stable
Contents:
Overview
Getting Started
User Functions
Core class
Visualization functions API
Generic functions
Dependencies
Data preparation
Input Data Format
Demo
DigitalCellSorter
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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P
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Q
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R
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S
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T
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V
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W
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Z
A
alignSeries() (DigitalCellSorter method)
annotate() (DigitalCellSorter method)
annotateWith_Hopfield_Scheme() (DigitalCellSorter method)
annotateWith_pDCS_Scheme() (DigitalCellSorter method)
annotateWith_ratio_Scheme() (DigitalCellSorter method)
B
batchEffectCorrection() (DigitalCellSorter method)
C
calculateQCmeasures() (DigitalCellSorter method)
calculateV() (DigitalCellSorter class method)
clean() (DigitalCellSorter method)
cluster() (DigitalCellSorter method)
convert() (DigitalCellSorter method)
convertColormap() (DigitalCellSorter class method)
createReverseDictionary() (DigitalCellSorter method)
D
df_expr() (DigitalCellSorter property)
DigitalCellSorter (class in DigitalCellSorter.core)
DigitalCellSorter.GenericFunctions (module)
DigitalCellSorter.ReadPrepareDataHCA (module)
E
extractFromZipOfGz() (in module DigitalCellSorter.GenericFunctions)
F
fileHDFpath() (DigitalCellSorter property)
G
geneListFileName() (DigitalCellSorter property)
getAnomalyScores() (DigitalCellSorter method)
getCells() (DigitalCellSorter method)
getCountsDataframe() (DigitalCellSorter method)
getDataframeByDonorID() (in module DigitalCellSorter.ReadPrepareDataHCA)
getElapsedTime() (in module DigitalCellSorter.GenericFunctions)
getExprOfCells() (DigitalCellSorter method)
getExprOfGene() (DigitalCellSorter method)
getHCAdataByURL() (in module DigitalCellSorter.ReadPrepareDataHCA)
getHugoName() (DigitalCellSorter method)
getIndexOfGoodQualityCells() (DigitalCellSorter method)
getNewMarkerGenes() (DigitalCellSorter method)
getQualityControlCutoff() (DigitalCellSorter method)
getStartTime() (in module DigitalCellSorter.GenericFunctions)
getSubnetworkOfPCN() (DigitalCellSorter method)
I
internalMakeMarkerSubplots() (VisualizationFunctions method)
K
KeyInFile() (DigitalCellSorter class method)
L
loadAnnotatedLabels() (DigitalCellSorter method)
loadExpressionData() (DigitalCellSorter method)
M
makeAnnotationResultsMatrixPlot() (VisualizationFunctions method)
makeAnomalyScoresPlot() (DigitalCellSorter method)
makeCellMarkersPiePlot() (VisualizationFunctions method)
makeHistogramNullDistributionPlot() (VisualizationFunctions method)
makeHopfieldLandscapePlot() (DigitalCellSorter method)
makeIndividualGeneExpressionPlot() (DigitalCellSorter method)
makeIndividualGeneTtestPlot() (DigitalCellSorter method)
makeMarkerExpressionPlot() (VisualizationFunctions method)
makeMarkerSubplots() (DigitalCellSorter method)
makePlotOfNewMarkers() (VisualizationFunctions method)
makeProjectionPlot() (VisualizationFunctions method)
makeProjectionPlotAnnotated() (DigitalCellSorter method)
makeProjectionPlotByBatches() (DigitalCellSorter method)
makeProjectionPlotByClusters() (DigitalCellSorter method)
makeProjectionPlotsQualityControl() (DigitalCellSorter method)
makeQualityControlHistogramPlot() (VisualizationFunctions method)
makeSankeyDiagram() (VisualizationFunctions method)
makeStackedBarplot() (VisualizationFunctions method)
makeTtestPlot() (VisualizationFunctions method)
mergeIndexDuplicates() (DigitalCellSorter method)
N
normalize() (DigitalCellSorter method)
P
prepare() (DigitalCellSorter method)
PrepareDataOnePatient_PREVIEW_DATASET() (in module DigitalCellSorter.ReadPrepareDataHCA)
prepareDemo5kData() (in module DigitalCellSorter.ReadPrepareDataHCA)
prepareMarkers() (DigitalCellSorter method)
process() (DigitalCellSorter method)
project() (DigitalCellSorter method)
propagateHopfield() (DigitalCellSorter method)
Q
qualityControl() (DigitalCellSorter method)
R
read() (in module DigitalCellSorter.GenericFunctions)
readMarkerFile() (DigitalCellSorter method)
readMTXdata() (in module DigitalCellSorter.core)
recordAnnotationResults() (DigitalCellSorter method)
recordExpressionData() (DigitalCellSorter method)
recordFilesOfIndividualDonors() (in module DigitalCellSorter.ReadPrepareDataHCA)
S
saveDir() (DigitalCellSorter property)
T
timeMark() (in module DigitalCellSorter.GenericFunctions)
V
visualize() (DigitalCellSorter method)
W
write() (in module DigitalCellSorter.GenericFunctions)
Z
zScoreOfSeries() (DigitalCellSorter class method)
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