Man pages for ludvigla/spaceST
spaceST
| batch.correct | Method batch.correct for spaceST class. |
| BuildTopicSNN | Build SNN graph |
| calc_cp10k | Calculate cp10k |
| CalcSNNSparse | Function to convert the knn graph into the snn graph. Stored... |
| cluster_matrix | Compute cluster matrix. |
| clusterST | Calculate clusters based on topics. |
| collect_gene_data | Collect data from bioMmRt |
| convert | Convert from ENSEMBL ID to HGNC symbol or MGI symbol |
| coordinates | get_coordinates: obtain spatial coordinates |
| counts | Method counts. |
| CreatespaceSTobject | Initiialize and setup the spaceST object |
| DE_heatmap | Plot DE heatmap |
| ExtractTopFeaturesST | Extract top features |
| filter | Method filter for spaceST class. |
| getLDA | Method topic.clusters. |
| heatmaps | Visualize spatial heatmaps |
| LDA | Helper function to compute lda using cellTree package. |
| merge | Merge and filter expression datasets |
| normcounts | Method normcounts. |
| palette.select | Create palettes |
| plot_QC_spaceST | Plot unique genes per feature and transcripts per feature. |
| RunDEspaceST | Run DE analysis using the edgeR package to detect... |
| RunModularityClusteringspaceST | Runs the modularity optimizer java program... |
| RunTSNEspaceST | t-SNE of spaceST data |
| SetIfNull | Helper function |
| smooth.viz | Smooth visualization of gene expression patterns |
| spaceST | The spaceST class. |
| spaceST-methods | space-ST methods. |
| spaceST-package | This package includes functions used to process, analyze and... |
| spaseST-methods | Method show for spaceST class. |
| spatial.clusters | Visualize spatial distribution of clusters. |
| SpatialNetwork | spaceST network graphs |
| spots_under_tissue | Method spots_under_tissue for spaceST class. |
| spPCA | Method spPCA for spaceST class. |
| ST_statistics | Quality Control statistics |
| ST_statistics_plot | Quality Control plot |
| tesselation.plot | Voronoi tesselation plot |
| tessViz | Plot tesselated object. |
| tiles2polygon | Convert tiles and add color. |
| topic.clusters | Method topic.clusters. |
| topic_heatmap | Plot heatmap of lda results. |
| var_genes | Detect variable genes using trendsceek package |
| volcano_plot_spaceST | Volcano plot |
