Man pages for sqjin/scAI
integrative analysis of single-cell transcriptomic and epigenomic profiles
| addpData | add the cell information into pData slot |
| as_matrix | Convert a sparse matrix to a dense matrix |
| bimodLikData | likelood ratio test |
| cellVisualization | visualize cells in 2D-dimensional space |
| clust2Mat | Convert membership into an adjacent matrix |
| create_scAIobject | creat a new scAI object |
| data_A549 | single cell multi-omics data of A549 cells. |
| data_kidney | single cell multi-omics data of kidney cells. |
| data_mESC | single cell multi-omics data of mESC cells. |
| data_simulation | simulated single cell multi-omics data. |
| data_simulation8 | A simulation dataset consists of five imbalanced cell... |
| DifferentialLRT | likelood ratio test |
| ExpMean | Calculate the mean of logged values |
| featureHeatmap | generate a heatmap for the expression of differential... |
| featureRankingPlot | Ranking the features (genes/loci) and show the top markers in... |
| featureScoreVisualization | visualize cells on the 2D space with features overlayed |
| featureVisualization | visualize cells on the 2D space with gene expression or... |
| findNearbyLoci | find the nearby loci in a given loci set for a given set of... |
| getAggregatedData | Generate the aggregated epigenomic data |
| getEmbeddings | compute the 2D coordinates of embeded cells, genes, loci and... |
| identifyClusterMarkers | Identify markers in each cell cluster |
| identifyClusters | Identify cell clusters |
| identifyFactorMarkers | Identify enriched features in each factor |
| inferRegulations | Infer regulatory relationships |
| lmHeatmap | Visualize the inferred biologically relevant factors We plot... |
| LogVMR | Calculate the variance to mean ratio of logged values |
| preprocessing | preprocess the raw.data including quality control and... |
| reducedDims | Perform dimensional reduction |
| reorderFeatures | Reorder features according to the loading values |
| runLeiden | Run Leiden clustering algorithm This code is modified from... |
| runPCA | Dimension reduction using PCA |
| run_scAI | run scAI model |
| runUMAP | Perform dimension reduction using UMAP |
| scAI-class | The scAI Class |
| scAImodel | Solving the optimization problem in scAI |
| scAI_theme_opts | ggplot theme in scAI |
| scPalette | Generate colors from a customed color palette |
| searchGeneRegions | find chromsome regions of genes |
| selectFeatures | select highly variable features |
| selectK | Select number of the rank |
| show-scAI-method | show method for scAI |
| VscAIplot | VscAI visualize the genes, loci and factors that separate... |
