armaCor | A slightly faster way of calculating column correlation... |
basicSeuratProc | Create and preprocess a Seurat object |
bestClusterThresholds | Find threshold of cluster detectability |
bestClusterTreeThresholds | Find threshold of cluster detectability in trees of clusters |
buildWijMatrix | Rescale the weights in an edge matrix to match a given... |
checkCountsWholeNumbers | Check that the count data contain only integer counts |
Conos | Conos R6 class |
convertToPagoda2 | Convert Conos object to Pagoda2 object |
edgeMat | Set edge matrix edgeMat with certain values on sample |
estimateWeightEntropyPerCell | Estimate entropy of edge weights per cell according to the... |
filter.genes.by.cluster.expression | Filter genes by requiring minimum average expression within... |
findSubcommunities | Increase resolution for a specific set of clusters |
getBetweenCellTypeCorrectedDE | Compare two cell types across the entire panel |
getBetweenCellTypeDE | Compare two cell types across the entire panel |
getCellNames | Access cell names from sample |
getClustering | Access clustering from sample |
getClusteringGroups | Extract specified clustering from list of conos clusterings |
getClusterRelationshipConsistency | Evaluate consistency of cluster relationships Using the... |
getCountMatrix | Access count matrix from sample |
getEmbedding | Access embedding from sample |
getGeneExpression | Access gene expression from sample |
getGenes | Access genes from sample |
getGlobalClusterMarkers | Deprecated; Get markers for global clusters |
getNeighborMatrix | Establish rough neighbor matching between samples given their... |
getOdGenesUniformly | Get top overdispersed genes across samples |
getOverdispersedGenes | Access overdispersed genes from sample |
getPca | Access PCA from sample |
getPerCellTypeDE | Do differential expression for each cell type in a conos... |
getPercentGlobalClusters | Evaluate how many clusters are global |
getRawCountMatrix | Access raw count matrix from sample |
getSampleNamePerCell | Retrieve sample names per cell |
greedyModularityCut | Performs a greedy top-down selective cut to optmize... |
multimulti.community | Constructrs a two-step clustering, first running... |
multitrap.community | Constructs a two-step clustering, first running... |
namedLevels | Get a vector with the levels of a factor named with their own... |
namedNames | Get a vector of the names of an object named by the names... |
p2app4conos | Utility function to generate a pagoda2 app from a conos... |
plotClusterBarplots | Plots barplots per sample of composition of each pagoda2... |
plotClusterBoxPlotsByAppType | Generate boxplot per cluster of the proportion of cells in... |
plotComponentVariance | Plot fraction of variance explained by the successive reduced... |
plotDEheatmap | Plot a heatmap of differential genes |
plotEmbeddings | Plot panel of specified embeddings |
plotSamples | Plot panel of specified embeddings, extracting them from... |
projectKNNs | Project a distance matrix into a lower-dimensional space. |
propagateLabelsDiffusion | Estimate labeling distribution for each vertex, based on... |
quickCCA | Perform CCA (using PMA package or otherwise) on two samples |
quickCPCA | Perform cpca on two samples |
quickPlainPCA | Use space of combined sample-specific PCAs as a space |
rawMatricesWithCommonGenes | Get raw matrices with common genes |
reexports | Objects exported from other packages |
saveConosForScanPy | Save Conos object on disk to read it from ScanPy |
saveDEasCSV | Save differential expression as table in *csv format |
saveDEasJSON | Save differential expression results as JSON |
scanKModularity | Scan joint graph modularity for a range of k (or k.self)... |
sgdBatches | Calculate the default number of batches for a given number of... |
small_panel.preprocessed | Small pre-processed data from Pagoda2, two samples, each... |
stableTreeClusters | Determine number of detectable clusters given a reference... |
velocityInfoConos | RNA velocity analysis on samples integrated with conos Create... |
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