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.
