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 |
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