Man pages for JEFworks-Lab/STdeconvolve
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
| annotateCellTypesGSEA | Match deconvolved cell-types to ground truth cell-types based... |
| 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... |
| getCorrMtx | Find Pearson's correlations between topics (cell-types) with... |
| getOverdispersedGenes | Normalize gene expression variance relative to... |
| 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... |
| restrictCorpus | Restrict to informative words (genes) for topic modeling |
| topGenes | Returns top n genes of each deconvolved cell-type for a given... |
| vizAllTopics | Visualize all topic proportions across pixels with... |
| vizGeneCounts | Visualize gene counts for a given gene in the pixels. Can... |
| vizTopic | Visualize pixel proportions of a single cell-type. |
