annotation_heatmap      Annotation Heatmap
compare_fits            Summarize and Compare Model Fits
de_analysis             Differential Expression Analysis using a Topic
                        Model
embedding_plot_2d       PCA, t-SNE and UMAP Plots
fit_multinom_model      Fit Simple Multinomial Model
fit_poisson_nmf         Fit Non-negative Matrix Factorization to Count
                        Data
fit_topic_model         Simple Interface for Fitting a Multinomial
                        Topic Model
loadings_plot           Loadings Plot
loglik_poisson_nmf      NMF and Topic Model Likelihoods and Deviances
merge_topics            Combine Topics in Multinomial Topic Model
multinom2poisson        Recover Poisson NMF Fit from Multinomial Topic
                        Model Fit
newsgroups              Topic modeling results from the "20 Newsgroups"
                        data set.
pbmc_facs               Mixture of 10 FACS-purified PBMC Single-Cell
                        RNA-seq data
pca_from_topics         Low-dimensional Embeddings from Poisson NMF or
                        Multinomial Topic Model
plot_loglik_vs_rank     Plot Log-Likelihood Versus Rank
plot_progress           Plot Progress of Model Fitting Over Time
poisson2multinom        Recover Multinomial Topic Model Fit from
                        Poisson NMF fit
predict.poisson_nmf_fit
                        Predict Methods for Poisson NMF and Multinomial
                        Topic Model
run_homer               Perform HOMER Motif Enrichment Analysis using
                        DE Genomic Positions
select.poisson_nmf_fit
                        Extract or Re-order Data Rows in Poisson NMF or
                        Multinomial Topic Model Fit
simulate_count_data     Simulate Count Data from Poisson NMF Model
simulate_poisson_gene_data
                        Simulate Gene Expression Data from Poisson NMF
                        or Multinomial Topic Model
simulate_toy_gene_data
                        Simulate Toy Gene Expression Data
structure_plot          Structure Plot
summary.poisson_nmf_fit
                        Summarize Poisson NMF or Multinomial Topic
                        Model Fit
volcano_plot            Volcano Plots for Visualizing Results of
                        Differential Expression Analysis
