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 perplexity. |
buildWijMatrix.CsparseMatrix |
Rescale the weights in an edge matrix to match a given perplexity. |
buildWijMatrix.TsparseMatrix |
Rescale the weights in an edge matrix to match a given perplexity. |
Conos |
Conos R6 class |
convertToPagoda2 |
Convert Conos object to Pagoda2 object |
edgeMat |
Set edge matrix edgeMat with certain values on sample |
edgeMat-method |
Set edge matrix edgeMat with certain values on sample |
edgeMat<- |
Set edge matrix edgeMat with certain values on sample |
edgeMat<--method |
Set edge matrix edgeMat with certain values on sample |
estimateWeightEntropyPerCell |
Estimate entropy of edge weights per cell according to the specified factor. Can be used to visualize alignment quality according to this factor. |
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 |
getCellNames-method |
Access cell names from sample |
getClustering |
Access clustering from sample |
getClustering-method |
Access clustering from sample |
getCountMatrix |
Access count matrix from sample |
getCountMatrix-method |
Access count matrix from sample |
getEmbedding |
Access embedding from sample |
getEmbedding-method |
Access embedding from sample |
getGeneExpression |
Access gene expression from sample |
getGeneExpression-method |
Access gene expression from sample |
getGenes |
Access genes from sample |
getGenes-method |
Access genes from sample |
getOverdispersedGenes |
Access overdispersed genes from sample |
getOverdispersedGenes-method |
Access overdispersed genes from sample |
getPca |
Access PCA from sample |
getPca-method |
Access PCA from sample |
getPerCellTypeDE |
Do differential expression for each cell type in a conos object between the specified subsets of apps |
getRawCountMatrix |
Access raw count matrix from sample |
getRawCountMatrix-method |
Access raw count matrix from sample |
getSampleNamePerCell |
Retrieve sample names per cell |
greedyModularityCut |
Performs a greedy top-down selective cut to optmize modularity |
p2app4conos |
Utility function to generate a pagoda2 app from a conos object |
plotClusterBarplots |
Plots barplots per sample of composition of each pagoda2 application based on selected clustering |
plotClusterBoxPlotsByAppType |
Generate boxplot per cluster of the proportion of cells in each celltype |
plotComponentVariance |
Plot fraction of variance explained by the successive reduced space components (PCA, CPCA) |
plotDEheatmap |
Plot a heatmap of differential genes |
projectKNNs |
Project a distance matrix into a lower-dimensional space. |
rawMatricesWithCommonGenes |
Get raw matrices with common genes |
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) values Builds graph with different values of k (or k.self if scan.k.self=TRUE), evaluating modularity of the resulting multilevel clustering NOTE: will run evaluations in parallel using con$n.cores (temporarily setting con$n.cores to 1 in the process) |
sgdBatches |
Calculate the default number of batches for a given number of vertices and edges. The formula used is the one used by the 'largeVis' reference implementation. This is substantially less than the recommendation E * 10000 in the original paper. |
small_panel.preprocessed |
Small pre-processed data from Pagoda2, two samples, each dimension (1000, 100) |
stableTreeClusters |
Determine number of detectable clusters given a reference walktrap and a bunch of permuted walktraps |
velocityInfoConos |
RNA velocity analysis on samples integrated with conos Create a list of objects to pass into gene.relative.velocity.estimates function from the velocyto.R package |