| compare_fits | Summarize and Compare Model Fits |
| cost | NMF and Topic Model Likelihoods and Deviances |
| deviance_poisson_nmf | NMF and Topic Model Likelihoods and Deviances |
| de_analysis | Differential Expression Analysis using a Topic Model |
| de_analysis_control_default | Differential Expression Analysis using a Topic Model |
| embedding_plot_2d | PCA, t-SNE and UMAP Plots |
| embedding_plot_2d_ggplot_call | 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_poisson_nmf_control_default | Fit Non-negative Matrix Factorization to Count Data |
| fit_topic_model | Simple Interface for Fitting a Multinomial Topic Model |
| init_poisson_nmf | Fit Non-negative Matrix Factorization to Count Data |
| init_poisson_nmf_from_clustering | Fit Non-negative Matrix Factorization to Count Data |
| loadings_plot | Loadings Plot |
| loadings_plot_ggplot_call | Loadings Plot |
| loglik_multinom_topic_model | NMF and Topic Model Likelihoods and Deviances |
| loglik_poisson_nmf | NMF and Topic Model Likelihoods and Deviances |
| loglik_vs_rank_ggplot_call | Plot Log-Likelihood Versus Rank |
| merge_topics | Combine Topics in Multinomial Topic Model |
| multinom2poisson | Recover Poisson NMF Fit from Multinomial Topic Model Fit |
| 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 |
| pca_hexbin_plot | PCA, t-SNE and UMAP Plots |
| pca_hexbin_plot_ggplot_call | PCA, t-SNE and UMAP Plots |
| pca_plot | PCA, t-SNE and UMAP Plots |
| plot.multinom_topic_model_fit | Structure Plot |
| plot.poisson_nmf_fit | Structure Plot |
| plot.topic_model_de_analysis | Volcano Plots for Visualizing Results of Differential Expression Analysis |
| 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.multinom_topic_model_fit | Predict Methods for Poisson NMF and Multinomial Topic Model |
| predict.poisson_nmf_fit | Predict Methods for Poisson NMF and Multinomial Topic Model |
| print.summary.multinom_topic_model_fit | Summarize Poisson NMF or Multinomial Topic Model Fit |
| print.summary.poisson_nmf_fit | Summarize Poisson NMF or Multinomial Topic Model Fit |
| run_homer | Perform HOMER Motif Enrichment Analysis using DE Genomic Positions |
| select | Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit |
| select.multinom_topic_model_fit | Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit |
| select.poisson_nmf_fit | Extract or Re-order Data Rows in Poisson NMF or Multinomial Topic Model Fit |
| select_loadings | 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_multinom_gene_data | Simulate Gene Expression Data from Poisson NMF or Multinomial Topic 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 |
| structure_plot_default_embed_method | Structure Plot |
| structure_plot_ggplot_call | Structure Plot |
| summary.multinom_topic_model_fit | Summarize Poisson NMF or Multinomial Topic Model Fit |
| summary.poisson_nmf_fit | Summarize Poisson NMF or Multinomial Topic Model Fit |
| tsne_from_topics | Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model |
| tsne_plot | PCA, t-SNE and UMAP Plots |
| umap_from_topics | Low-dimensional Embeddings from Poisson NMF or Multinomial Topic Model |
| umap_plot | PCA, t-SNE and UMAP Plots |
| volcano_plot | Volcano Plots for Visualizing Results of Differential Expression Analysis |
| volcano_plotly | Volcano Plots for Visualizing Results of Differential Expression Analysis |
| volcano_plot_do_label_default | Volcano Plots for Visualizing Results of Differential Expression Analysis |
| volcano_plot_ggplot_call | Volcano Plots for Visualizing Results of Differential Expression Analysis |
| volcano_plot_ly_call | Volcano Plots for Visualizing Results of Differential Expression Analysis |