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 |