API for conos
Clustering on Network of Samples

Global functions
Conos Man page
Rjnmf Source code
RjnmfC Source code
adjacent_vertex_weights Source code
adjacent_vertices Source code
adjustMatrixRownames Source code
adjustWeightsByCellBalancing Source code
adjustWeightsByCellBalancingC Source code
aggregateDEMarkersAcrossDatasets Source code
as_factor Source code
basicSeuratProc Man page
bestClusterThresholds Man page Source code
bestClusterTreeThresholds Man page Source code
buildWijMatrix Man page Source code
buildWijMatrix.CsparseMatrix Man page Source code
buildWijMatrix.TsparseMatrix Man page Source code
checkBits Source code
checkCountsWholeNumbers Man page
checkOpenMP Source code
colSumByFactor Source code
collapseCellsByType Man page Source code
commonOverdispersedGenes Source code
complete.dend Source code
convertDistanceToSimilarity Source code
convertToPagoda2 Man page
cpcaF Source code
cpcaFast Source code
edgeMat Man page
edgeMat,Pagoda2-method Man page
edgeMat,Seurat-method Man page
edgeMat,seurat-method Man page
edgeMat<- Man page
edgeMat<-,Pagoda2-method Man page
edgeMat<-,Seurat-method Man page
edgeMat<-,seurat-method Man page
embedGraphUmap Source code
embedKnnGraph Source code
embeddingPlot Man page
estimateWeightEntropyPerCell Man page
extendMatrix Source code
factorBreakdown Source code
findSubcommunities Man page
generateDEMatrixMetadata Source code
getBetweenCellTypeCorrectedDE Man page Source code
getBetweenCellTypeDE Man page Source code
getCellNames Man page
getCellNames,Conos-method Man page
getCellNames,Pagoda2-method Man page
getCellNames,Seurat-method Man page
getCellNames,seurat-method Man page
getClusterRelationshipConsistency Man page Source code
getClustering Man page
getClustering,Conos-method Man page
getClustering,Pagoda2-method Man page
getClustering,Seurat-method Man page
getClustering,seurat-method Man page
getClusteringGroups Man page Source code
getCountMatrix Man page
getCountMatrix,Pagoda2-method Man page
getCountMatrix,Seurat-method Man page
getCountMatrix,seurat-method Man page
getDecoyProjections Source code
getEmbedding Man page
getEmbedding,Conos-method Man page
getEmbedding,Pagoda2-method Man page
getEmbedding,Seurat-method Man page
getEmbedding,seurat-method Man page
getGeneExpression Man page
getGeneExpression,Conos-method Man page
getGeneExpression,Pagoda2-method Man page
getGenes Man page
getGenes,Conos-method Man page
getGenes,Pagoda2-method Man page
getGenes,Seurat-method Man page
getGenes,seurat-method Man page
getGlobalClusterMarkers Man page
getLocalEdges Source code
getLocalNeighbors Source code
getNeighborMatrix Man page Source code
getOdGenesUniformly Man page Source code
getOverdispersedGenes Man page
getOverdispersedGenes,Conos-method Man page
getOverdispersedGenes,Pagoda2-method Man page
getOverdispersedGenes,Seurat-method Man page
getOverdispersedGenes,seurat-method Man page
getPca Man page
getPca,Pagoda2-method Man page
getPca,Seurat-method Man page
getPca,seurat-method Man page
getPcaBasedNeighborMatrix Source code
getPerCellTypeDE Man page Source code
getPercentGlobalClusters Man page Source code
getRawCountMatrix Man page
getRawCountMatrix,Conos-method Man page
getRawCountMatrix,Pagoda2-method Man page
getRawCountMatrix,Seurat-method Man page
getRawCountMatrix,seurat-method Man page
getSampleNamePerCell Man page
getSumWeightMatrix Source code
get_nearest_neighbors Source code
graphToAdjList Source code
greedyModularityCut Man page Source code
greedyModularityCutC Source code
leiden.community Man page
maxStableClusters Source code
mergeCountMatrices Source code
multimulti.community Man page Source code
multitrap.community Man page Source code
namedLevels Man page Source code
namedNames Man page Source code
p2app4conos Man page
papply Source code
pareDownHubEdges Source code
plotClusterBarplots Man page
plotClusterBoxPlotsByAppType Man page
plotComponentVariance Man page
plotDEheatmap Man page
plotEmbeddings Man page Source code
plotSamples Man page Source code
projectKNNs Man page Source code
projectSamplesOnGlobalAxes Source code
propagateLabelsDiffusion Man page
propagate_labels Source code
quickCCA Man page Source code
quickCPCA Man page Source code
quickJNMF Source code
quickNULL Source code
quickPlainPCA Man page Source code
rawMatricesWithCommonGenes Man page Source code
rbindDEMatrices Source code
reduceEdgesInGraph Source code
reduceEdgesInGraphIteratively Source code
reexports Man page
referenceWij Source code
saveConosForScanPy Man page
saveDEasCSV Man page Source code
saveDEasJSON Man page Source code
scaledMatrices Source code
scaledMatricesP2 Source code
scaledMatricesSeurat Source code
scaledMatricesSeuratV3 Source code
scanKModularity Man page
scoreTreeConsistency Source code
sgd Source code
sgdBatches Man page Source code
small_panel.preprocessed Man page
smooth_count_matrix Source code
sn Source code
spcov Source code
splitVectorByNodes Source code
stableTreeClusters Man page Source code
treeJaccard Source code
validateBetweenCellTypeParams Source code
validatePerCellTypeParams Source code
conos documentation built on Feb. 23, 2021, 9:06 a.m.