Man pages for conos
Clustering on Network of Samples

basicSeuratProcCreate and preprocess a Seurat object
bestClusterThresholdsFind threshold of cluster detectability
bestClusterTreeThresholdsFind threshold of cluster detectability in trees of clusters
buildWijMatrixRescale the weights in an edge matrix to match a given...
checkCountsWholeNumbersCheck that the count data contain only integer counts
collapseCellsByTypeCollapse count matrices by cell type, given min/max number of...
ConosConos R6 class
convertToPagoda2Convert Conos object to Pagoda2 object
edgeMatSet edge matrix edgeMat with certain values on sample
estimateWeightEntropyPerCellEstimate entropy of edge weights per cell according to the...
findSubcommunitiesIncrease resolution for a specific set of clusters
getBetweenCellTypeCorrectedDECompare two cell types across the entire panel
getBetweenCellTypeDECompare two cell types across the entire panel
getCellNamesAccess cell names from sample
getClusteringAccess clustering from sample
getClusteringGroupsExtract specified clustering from list of conos clusterings
getClusterRelationshipConsistencyEvaluate consistency of cluster relationships Using the...
getCountMatrixAccess count matrix from sample
getEmbeddingAccess embedding from sample
getGeneExpressionAccess gene expression from sample
getGenesAccess genes from sample
getGlobalClusterMarkersDeprecated; Get markers for global clusters
getNeighborMatrixEstablish rough neighbor matching between samples given their...
getOdGenesUniformlyGet top overdispersed genes across samples
getOverdispersedGenesAccess overdispersed genes from sample
getPcaAccess PCA from sample
getPerCellTypeDEDo differential expression for each cell type in a conos...
getPercentGlobalClustersEvaluate how many clusters are global
getRawCountMatrixAccess raw count matrix from sample
getSampleNamePerCellRetrieve sample names per cell
greedyModularityCutPerforms a greedy top-down selective cut to optmize...
multimulti.communityConstructrs a two-step clustering, first running...
multitrap.communityConstructs a two-step clustering, first running...
namedLevelsGet a vector with the levels of a factor named with their own...
namedNamesGet a vector of the names of an object named by the names...
p2app4conosUtility function to generate a pagoda2 app from a conos...
plotClusterBarplotsPlots barplots per sample of composition of each pagoda2...
plotClusterBoxPlotsByAppTypeGenerate boxplot per cluster of the proportion of cells in...
plotComponentVariancePlot fraction of variance explained by the successive reduced...
plotDEheatmapPlot a heatmap of differential genes
plotEmbeddingsPlot panel of specified embeddings
plotSamplesPlot panel of specified embeddings, extracting them from...
projectKNNsProject a distance matrix into a lower-dimensional space.
propagateLabelsDiffusionEstimate labeling distribution for each vertex, based on...
quickCCAPerform CCA (using PMA package or otherwise) on two samples
quickCPCAPerform cpca on two samples
quickPlainPCAUse space of combined sample-specific PCAs as a space
rawMatricesWithCommonGenesGet raw matrices with common genes
reexportsObjects exported from other packages
saveConosForScanPySave Conos object on disk to read it from ScanPy
saveDEasCSVSave differential expression as table in *csv format
saveDEasJSONSave differential expression results as JSON
scanKModularityScan joint graph modularity for a range of k (or k.self)...
sgdBatchesCalculate the default number of batches for a given number of...
small_panel.preprocessedSmall pre-processed data from Pagoda2, two samples, each...
stableTreeClustersDetermine number of detectable clusters given a reference...
conos documentation built on Feb. 23, 2021, 9:06 a.m.