Man pages for compbiomed/animalcules
Interactive microbiome analysis toolkit

alpha_div_boxplotAlpha diversity boxplot
alpha_div_testGet alpha diversity
animalcules-packageanimalcules: Interactive microbiome analysis toolkit
counts_to_logcpmCovert a counts table to a relative abundances table
counts_to_relabuCovert a counts table to a relative abundances table
df_char_to_factorFactorize all categorical columns
differential_abundanceDifferential abundance analysis
dimred_pcaDimensionality reduction through PCA
dimred_pcoaDimensionality reduction through PCoA
dimred_tsneDimensionality reduction through t-SNE
dimred_umapDimensionality reduction through PCA
diversitiesGet alpha diversity
diversities_helpGet alpha diversity
diversity_beta_boxplotBeta diversity boxplot
diversity_beta_heatmapBeta diversity heatmap
diversity_beta_testBeta diversity test (by default we use bray-curtis distance)
do_alpha_div_testAlpha diversity statistical test
filter_categorizeCategorize continuous variables
filter_summary_bar_densityData visualization by bar plot / density plot
filter_summary_pie_boxData visualization by pie chart / box plot
find_biomarkerIdentify biomarkers
find_taxon_matFind the Taxonomy Information Matrix
find_taxonomyFind the taxonomy for unlimited tids
find_taxonomy_300Find the taxonomy for maximum 300 tids
gini_simpsonGet alpha diversity using gini
grep_tidGreps the tid from the given identifier string
inverse_simpsonGet alpha diversity using inverse simpson
is_categoricalCheck if object is categorical
is_integer0check if integer(0)
is_integer1check if integer(1)
mae_pick_organismsModify organisms of multi-assay experiment object
mae_pick_samplesModify samples of multi-assay experiment object
pct2strConverts decimal percentage to string with specified digits
percentFormat decimals to percentages
read_pathoscope_dataReads the data from PathoScope reports and returns a list of...
relabu_barplotPlot bar plots of sample and group level relative abundance
relabu_boxplotPlot boxplots comparing different organism prevalence across...
relabu_heatmapPlot heatmap of sample level counts in logcpm
run_animalculesRun animalcules shiny app
shannonGet alpha diversity using shannon
simpson_indexGet alpha diversity using simpson
upsample_countsUpsample a counts table to a higher taxon level
write_to_biomOutput biom
compbiomed/animalcules documentation built on June 23, 2020, 9:52 a.m.