Man pages for BaderLab/scClustViz
Differential Expression-based scRNAseq Cluster Assessment and Viewing
| addCellMarkersToCGS | Add gene symbols and cell type marker information to cluster... |
| CalcAllSCV | Prepare all cluster solutions for visualization with... |
| CalcCGS | Calculate cluster-wise gene statistics for sCVdata |
| CalcDEcombn | Performs DE testing between pairs of clusters in sCVdata |
| CalcDEvsRest | Calculates one vs. all DE tests for sCVdata |
| CalcSCV | Create sCVdata object with calculation results for a cluster |
| CalcSilhouette | Calculates silhouette widths for all cells in sCVdata |
| ColNNZ | Count non-zero entries per column of a matrix |
| cosineSim | Computes the cosine similarity between two vectors |
| DEdist | Calculate inter-cluster distances |
| DEdistNN | Determine nearest neighbouring clusters |
| DEmarker | Find marker genes for each cluster |
| DEneighb | Find differentially expressed genes between nearest... |
| dotplotDEgenes | scClustViz plot helper function: Return DE genes per cluster |
| findKeyType | Automatically determines keytype for AnnotationDb lookup |
| fx_calcCGS | Internal fx for cluster-wise gene statistics |
| fx_calcCGS_BP | Internal fx for cluster-wise gene statistics using... |
| fx_calcDEcombn | Internal fx to calculate DE between combinations of clusters |
| fx_calcDEcombn_BP | Internal fx to calculate DE between combinations of clusters... |
| fx_calcDEcombn_slow | Internal fx to calculate DE between combinations of clusters... |
| fx_calcDEvsRest | Internal fx to perform one vs all DE testing |
| fx_calcDEvsRest_BP | Internal fx to perform one vs all DE testing using... |
| fx_calcDEvsRest_slow | Internal fx to perform one vs all DE testing using base R |
| fx_calcDist_cellEmb | Internal function for distance between clusters from cell... |
| fx_calcDist_geneExpr | Internal function for distance between clusters by gene... |
| fx_calcDist_numDE | Internal function for distance between clusters by number of... |
| fx_calcDist_scoreDE | Internal function for distance between clusters by DE score. |
| fx_calcEScombn | Internal fx to calculate genes used for deVS calculation |
| fx_calcESvsRest | Internal fx to calculate logGER for DEvsRest calculation |
| fx_calcESvsRest_BP | Internal fx to calculate logGER for DEvsRest calculation... |
| fx_calcMarker | Internal function to find marker genes for each cluster |
| fx_calcNeighb | Internal function to find DE genes between nearest... |
| fx_calcSilhouette | Internal fx to call 'silhouette' for sCVdata. |
| getEmb | Get cell embeddings from input data object |
| getExpr | Get gene expression matrix from input data object |
| getMD | Get metadata from input data object |
| hasEmb | List cell embedding types from input data object |
| labelCellTypes | scClustViz helper fx: Add predicted cell type names to... |
| map2symbol | Maps gene identifiers to official gene symbol |
| meanLogX | Computes the mean of log-scaled values |
| origin.label.dist | Internal fx to calc dist from point to label end |
| overlap.edge | Internal fx to calc overlap of label and plot edge |
| overlap.proportion.point | Internal fx to calc relative overlap of labels |
| plot_clusterGenes_DEgenes | scClustViz plot: Plot within-cluster gene expression... |
| plot_clusterGenes_markers | scClustViz plot: Plot within-cluster gene expression... |
| plot_clusterGenes_search | scClustViz plot: Plot within-cluster gene expression... |
| plot_clustSep | scClustViz plot: Cluster separation boxplots |
| plot_compareClusts | scClustViz plot: Volcano and MA-style plots to compare... |
| plot_deDotplot | scClustViz plot: Plot gene expression dotplots. |
| plot_GEboxplot | scClustViz plot: Compare gene expression across clusters |
| plot_mdCompare | scClustViz plot: Plot to compare cell metadata |
| plot_mdPerClust | scClustViz plot: Plot to view cellular metadata by cluster |
| plot_sil | scClustViz plot: Silhouette plot |
| plot_tsne | scClustViz plot: Plot cell embedding in 2D |
| RowNNZ | Count non-zero entries per row of a matrix |
| runShiny | Run the scClustViz Shiny app |
| scClustViz | scClustViz: A package for interactive exploration of scRNAseq... |
| sCVdata-class | Analysis results for the scClustViz app |
| sCVparams-class | Parameters used in the sCVdata class and methods. |
| spreadLabels2 | Prevent overlapping labels |
| subsetCells | Subset a data object to return just the specified cells |
| tsne_labels | scClustViz plot element: Cluster names on cluster centroid. |
