# Interactive microbiome analysis toolkit

## Documentation for package ‘animalcules’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

alpha_div_boxplot | Alpha diversity boxplot
alpha_div_test | Get alpha diversity
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_taxonomy | Find the taxonomy for unlimited tids
find_taxonomy_300 | Find the taxonomy for maximum 300 tids
find_taxon_mat | Find the Taxonomy Information Matrix
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 final guess relative abundance and count data
relabu_barplot | Plot bar plots of sample and group level relative abundance
relabu_boxplot | Plot boxplots comparing different organism prevalence across conditions
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