# Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

## Documentation for package ‘STdeconvolve’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.