Man pages for biobakery/anpan
Quantifying Microbial Strain-Host Associations
| anpan | Run anpan |
| anpan_batch | Apply anpan to a many bugs |
| anpan_pglmm | Run a phylogenetic generalized linear mixed model |
| anpan_pglmm_batch | Run PGLMMs on a batch of tree files |
| anpan_pwy_ranef | Estimate a species-pathway abundance random effects model |
| anpan_pwy_ranef_batch | Fit the pathway random effects model for multiple bugs |
| anpan_repeated_measures | Use repeated measures to refine the gene model |
| anpan_subjectwise_pglmm | Fit a subject-wise PGLMM |
| anpan_vignette | Open the anpan vignette |
| compute_clade_effects | Compute a clade effect |
| filter_batch | Filter a batch of files |
| filter_gf | Filter a gene family file |
| get_cor_mat | Get the correlation matrix of a tree |
| get_genome_intersect_counts | Get genome intersection counts |
| olap_tree_and_meta | Overlap a tree and metadata |
| plot_cor_mat | Plot a correlation matrix Generate a colorful heatmap... |
| plot_elpd_diff | Plot the ELPD difference interval |
| plot_genome_intersection_histograms | Intersection histograms |
| plot_genome_intersections | Plot genome intersections |
| plot_half_cor_mat | Plot a rotated half correlation matrix |
| plot_lines | Make a filter-labelled line plot |
| plot_outcome_tree | Plot a tree file showing the outcome variable |
| plot_p_value_histogram | Make a p-value histogram |
| plot_pwy_ranef | Plot a pathway random effects result |
| plot_pwy_ranef_intervals | Plot a pathway random effects result |
| plot_results | Plot the data for top results |
| plot_tree_with_post | Plot a tree and the PGLMM posterior on phylogenetic effects |
| plot_tree_with_post_pred | Plot a tree and the PGLMM posterior predictive |
| read_and_filter | Read and filter a gene family file |
| read_bug | Read a bug's genefamily file |
