| annotateCellTypesGSEA | Match deconvolved cell-types to ground truth cell-types based on transcriptional profiles |
| cleanCounts | Filter a counts matrix |
| correlationPlot | Generate heatmap of correlations |
| fitLDA | Find the optimal number of cell-types K for the LDA model |
| getBetaTheta | Pull out cell-type proportions across pixels (theta) and cell-type gene probabilities (beta) matrices from fitted LDA models from fitLDA |
| getCorrMtx | Find Pearson's correlations between topics (cell-types) with respect to their proportions across documents (pixels), i.e. thetas, or gene probabilities, i.e. betas. |
| getOverdispersedGenes | Normalize gene expression variance relative to transcriptome-wide expectations (Modified from SCDE/PAGODA2 code) |
| lsatPairs | Function to get Hungarian sort pairs via clue::lsat |
| mOB | Spatial transcriptomics of the mouse olfactory bulb |
| optimalModel | Get the optimal LDA model |
| perplexityPlot | Plot the perplexity and rare cell-types versus fitted Ks |
| preprocess | Pre-process ST pixel gene count matrices to construct corpus for input into LDA |
| restrictCorpus | Restrict to informative words (genes) for topic modeling |
| topGenes | Returns top n genes of each deconvolved cell-type for a given beta matrix |
| vizAllTopics | Visualize all topic proportions across pixels with 'scatterpie' |
| vizGeneCounts | Visualize gene counts for a given gene in the pixels. Can also see group assignment of spots. |
| vizTopic | Visualize pixel proportions of a single cell-type. |