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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_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
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 |