Man pages for animalcules
Interactive microbiome analysis toolkit
| alpha_div_boxplot | Alpha diversity boxplot |
| alpha_div_test | Get alpha diversity |
| animalcules-package | animalcules: Interactive microbiome analysis toolkit |
| counts_to_logcpm | Covert a counts table to a relative abundances table |
| counts_to_relabu | Covert a counts table to a relative abundances table |
| df_char_to_factor | Factorize all categorical columns |
| differential_abundance | Differential abundance analysis |
| dimred_pca | Dimensionality reduction through PCA |
| dimred_pcoa | Dimensionality reduction through PCoA |
| dimred_tsne | Dimensionality reduction through t-SNE |
| dimred_umap | Dimensionality reduction through PCA |
| diversities | Get alpha diversity |
| diversities_help | Get alpha diversity |
| diversity_beta_boxplot | Beta diversity boxplot |
| diversity_beta_heatmap | Beta diversity heatmap |
| diversity_beta_test | Beta diversity test (by default we use bray-curtis distance) |
| do_alpha_div_test | Alpha diversity statistical test |
| filter_categorize | Categorize continuous variables |
| filter_summary_bar_density | Data visualization by bar plot / density plot |
| filter_summary_pie_box | Data visualization by pie chart / box plot |
| find_biomarker | Identify biomarkers |
| find_taxon_mat | Find the Taxonomy Information Matrix |
| find_taxonomy | Find the taxonomy for unlimited tids |
| find_taxonomy_300 | Find the taxonomy for maximum 300 tids |
| gini_simpson | Get alpha diversity using gini |
| grep_tid | Greps the tid from the given identifier string |
| inverse_simpson | Get alpha diversity using inverse simpson |
| is_categorical | Check if object is categorical |
| is_integer0 | check if integer(0) |
| is_integer1 | check if integer(1) |
| mae_pick_organisms | Modify organisms of multi-assay experiment object |
| mae_pick_samples | Modify samples of multi-assay experiment object |
| pct2str | Converts decimal percentage to string with specified digits |
| percent | Format decimals to percentages |
| read_pathoscope_data | Reads the data from PathoScope reports and returns a list of... |
| relabu_barplot | Plot bar plots of sample and group level relative abundance |
| relabu_boxplot | Plot boxplots comparing different organism prevalence across... |
| relabu_heatmap | Plot heatmap of sample level counts in logcpm |
| run_animalcules | Run animalcules shiny app |
| shannon | Get alpha diversity using shannon |
| simpson_index | Get alpha diversity using simpson |
| upsample_counts | Upsample a counts table to a higher taxon level |
| write_to_biom | Output biom |
