Man pages for kharchenkolab/conos
Clustering on Network of Samples
| 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... |
