edroaldo/fusca
Framework for Unified Single-Cell Analysis

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287
Source code
85
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143
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API

API for edroaldo/fusca
Framework for Unified Single-Cell Analysis

Global functions
%>% Man page
.onLoad Source code
AddAssay Man page Source code
CellComm Man page
CellComm-class Man page
CellComm-initialize,initializeCellComm Man page
CellRouter Man page
CellRouter-class Man page
CreateAssay Source code
CreateCellComm Man page Source code
CreateCellRouter Man page Source code
FindVariableGenes Man page Source code
FuscaAssay Man page
FuscaAssay-class Man page
Normalize Man page
Normalize,CellRouter-method Man page
StatBag Man page
activeSignaling Man page Source code
addInfo Man page Source code
apply1_sp Man page Source code
apply2_sp Man page Source code
buildGRN Man page
buildGRN,CellRouter-method Man page
buildGRN2 Man page
buildGRN2,CellRouter-method Man page
buildKNN Man page
buildKNN,CellRouter-method Man page
cRamp Man page Source code
cRamp2 Man page Source code
cRampClust Man page Source code
calculateCentroids Man page
calculateCentroids,CellRouter-method Man page
calculateDistanceMatrix Man page
calculateDistanceMatrix,CellRouter-method Man page
calculateLigandReceptor Man page Source code
calculateObservedMean Man page Source code
calculatePvalue Man page Source code
cellnetwork3 Man page Source code
cellnetworksPPI Man page Source code
cellnetworksPPI2 Man page Source code
center_with_threshold Man page Source code
clusterGenesPseudotime Man page
clusterGenesPseudotime,CellRouter-method Man page
clusterPermutation Man page Source code
clusterPermutationSubcluster Man page Source code
clustergenes Man page Source code
cn_sampR_to_pattern Man page
cn_testPattern Man page Source code
commToNames Man page Source code
compareTwoGroups Man page
compareTwoGroups,CellRouter-method Man page
computeDC Man page Source code
computeFC Man page
computeFC,CellRouter-method Man page
computePCA Man page
computePCA,CellRouter-method Man page
computeTSNE Man page
computeTSNE,CellRouter-method Man page
computeUMAP Man page
computeUMAP,CellRouter-method Man page
computeValue Man page
computeValue,CellRouter-method Man page
computeValueSubclusters Man page
computeValueSubclusters,CellRouter-method Man page
convertID Man page Source code
convertIDs Man page Source code
correlationPseudotime Man page
correlationPseudotime,CellRouter-method Man page
createNetworksFromPaths Man page Source code
createPPI Man page Source code
createPaths Man page Source code
createTFNetwork Man page Source code
curves_info Man page
customSpace Man page
customSpace,CellRouter-method Man page
detectGenes Source code
dotplot Man page
dotplot,CellRouter-method Man page
dotplotByMetadata Man page
dotplotByMetadata,CellRouter-method Man page
dotplotSignatureScore Man page
dotplotSignatureScore,CellRouter-method Man page
extractRegulators Man page Source code
filterCells Man page Source code
findClusters Man page
findClusters,CellRouter-method Man page
findCurves Man page
findCurves,CellRouter-method Man page
findPaths Man page
findPaths,CellRouter-method Man page
findPathsRJava Man page
findPathsRJava,CellRouter-method Man page
findSignatures Man page Source code
findSubclusters Man page
findSubclusters,CellRouter-method Man page
find_curve Man page Source code
find_sequence Man page Source code
find_tfs Man page Source code
findmarkers Man page
findpaths.simple Man page
findpaths.simple,CellComm-method Man page
findpaths.simpleRJava Man page
findpaths.simpleRJava,CellComm-method Man page
geom_spatial Source code
getIndexes Man page Source code Source code
globalGRN Man page Source code
graphClustering Man page
graphClustering,CellRouter-method Man page
grnScoresHeatmap Man page
grnScoresHeatmap,CellRouter-method Man page
grnscores Man page
grnscores,CellRouter-method Man page
ig_tabToIgraph Man page Source code
initialize,CellComm-method Man page
interactionmatrix Man page Source code
mat_zscores Man page Source code
modelClustering Man page
multiplot Man page Source code
nodeLabels Man page Source code
pathsinfo Man page
pathwaycluster Man page
pathwaycluster,CellRouter-method Man page
pathwayenrichment Man page
pathwayenrichment,CellRouter-method Man page
plotClusterHeatmap Man page
plotClusterHeatmap,CellRouter-method Man page
plotClusterProfiler Man page Source code
plotClusters Man page
plotClusters,CellRouter-method Man page
plotDRExpression Man page
plotDRExpression,CellRouter-method Man page
plotDRExpression2 Man page
plotDRExpression2,CellRouter-method Man page
plotEnrichR Man page Source code
plotGenesInClusters Man page Source code
plotGenesInClusters,list-method Man page
plotIntegration Man page Source code
plotInteractionMatrix2 Man page Source code
plotInteractionNetwork Man page Source code
plotKNN Man page
plotKNN,CellRouter-method Man page
plotPairDotplot Man page Source code
plotPathHeatmap Man page
plotPathHeatmap,CellRouter-method Man page
plotProportion Man page Source code
plotProportion2 Man page Source code
plotReducedDimension Man page Source code
plotRegulonDynamics Man page
plotRegulonDynamics,CellRouter-method Man page
plotSelectedClusters Man page Source code
plotSignatureScore Man page
plotSignatureScore,CellRouter-method Man page
plotSignatureScoreDynamics Man page
plotSignatureScoreDynamics,CellRouter-method Man page
plotSignaturesBoxplot Man page Source code
plotSignaturesHeatmap Man page Source code
plotSpatialClusters Man page Source code
plotSpatialExpression Man page Source code
plotSpatialScore Man page
plotSpatialScore,CellRouter-method Man page
plotSpatialSubclusters Man page Source code
plotValue Man page
plotValue,CellRouter-method Man page
plotViolin Man page Source code
plotbranch Man page
plotbranch,CellRouter-method Man page
plotpaths Man page
plotpaths,CellRouter-method Man page
plottr Man page
plottr,CellRouter-method Man page
plottrajectories Man page
plottrajectories,CellRouter-method Man page
plottrajectory Man page
plottrajectory,CellRouter-method Man page
population.pairing Man page Source code
predictCellCycle Man page Source code
predictCellInteractions Man page Source code
predictState Man page Source code
processCurves Man page
processCurves,CellRouter-method Man page
processTrajectories Man page
processTrajectories,CellRouter-method Man page
range01 Man page Source code
rankGenesTranscriptionalClusters Man page
rankGenesTranscriptionalClusters,CellRouter-method Man page
ranked_findSpecGenes Man page
rankpaths Man page Source code
read10X Man page Source code
read10XImage Man page
read10XImage,CellRouter-method Man page
regulatornetwork Man page Source code
scale.sparse Man page Source code
scaleData Man page
scaleData,CellRouter-method Man page
scoreGeneSets Man page Source code
signaling2TF Man page Source code
smoothDynamics Man page
smoothDynamics,CellRouter-method Man page
sourcestargets Man page Source code
sparse.cor Man page Source code
sparse.cor2 Man page Source code
stat_bag Man page Source code
subsetCells Source code
summarize.flow Man page Source code
testExport Man page Source code
topGenes Man page
topGenes,CellRouter-method Man page
verify_gene_exp Man page Source code
edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.

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