# A Pipeline for Microbiome Analysis and Visualization

## Documentation for package ‘tidyMicro’ version 1.43

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

## Help Pages

alpha_div | Alpha Diversity Calculations for tidy_micro
bb_bars | Create stacked bar charts based on beta binomial model estimates
bb_mods | Fit beta binomial models to each taxa within an OTU table
beta_div | Beta Diversity Calculations for tidy_micro
beta_heatmap | Create heatmaps of the supplied dissimilarity matrices
cla | An OTU table of class level taxa counts
clin | A data set containing the clinical data of the subjects sequenced
cor_heatmap | Create correlation heatmaps of taxa and another continuous variable
cor_rocky_mtn | Create Rocky Mountain plots from taxa relative abundance correlations
fam | An OTU table of family level taxa counts
micro_alpha_reg | Linear regression on alpha diversities within a micro_set
micro_chisq | Run Chi-Squared tests for each taxa
micro_forest | Create forest plots from negative binomial taxa models
micro_heatmap | Create heatmaps of estiamted coefficients from negative binomial models
micro_pca | Calculate and plot principle components
micro_PERMANOVA | A function to run PERMANOVA on tidi_micro data sets
micro_rank_sum | Run rank sum tests for each taxa within an OTU table
micro_rocky_mtn | Create Rocky Mountain plots from negative binomial taxa models
nb_bars | Create stacked bar charts based on negative binomial model estimates
nb_mods | Fit negative binomial models to each taxa within an OTU table
ord | An OTU table of order level taxa counts
otu_filter | A function to aggregate low prevalence, abundance, or unwanted taxa together
pca_3d | Create 3d PCA plots
phy | An OTU table of phylum level taxa counts
ra_bars | Function to make stacked bar charts of taxa relative abundance
taxa_boxplot | Function to make boxplots of taxa counts or relative abundance
taxa_summary | Summarize the information
three_mode | Create Three Mode PCA and PCoA plots
tidy_micro | A function to merge multiple OTU tables and clinical data into a "tidy" format