Learn R Programming
⚠️There's a newer version (1.47) of this package.Take me there.

tidyMicro

A pipeline for microbiome analysis and visualization

Main Features

  • Merge any number OTU tables with clinical data into one tidy data set

  • Data visualization for exploration

  • Calculate, analyze, and visualize diversity measures

  • Fit negative binomial, beta binomial, rank sum, and presence absence models

  • Create stacked bar charts based on negative binomial and beta binomial model estimates

  • Longitudinal and Three Mode PCA plots

Intallation

# install.packages("devtools")
devtools::install_github("CharlieCarpenter/tidyMicro")

Copy Link

Version

Install

install.packages('tidyMicro')

Monthly Downloads

5

Version

1.43

License

GPL-3

Maintainer

Charlie Carpenter

Last Published

March 28th, 2020

Functions in tidyMicro (1.43)

fam

An OTU table of family level taxa counts
micro_alpha_reg

Linear regression on alpha diversities within a micro_set
micro_rocky_mtn

Create Rocky Mountain plots from negative binomial taxa models
micro_PERMANOVA

A function to run PERMANOVA on tidi_micro data sets
nb_bars

Create stacked bar charts based on negative binomial model estimates
micro_rank_sum

Run rank sum tests for each taxa within an OTU table
micro_pca

Calculate and plot principle components
nb_mods

Fit negative binomial models to each taxa within an OTU table
micro_heatmap

Create heatmaps of estiamted coefficients from negative binomial models
micro_chisq

Run Chi-Squared tests for each taxa
micro_forest

Create forest plots from negative binomial taxa models
three_mode

Create Three Mode PCA and PCoA plots
taxa_boxplot

Function to make boxplots of taxa counts or relative abundance
%>%

Pipe operator
ra_bars

Function to make stacked bar charts of taxa relative abundance
otu_filter

A function to aggregate low prevalence, abundance, or unwanted taxa together
ord

An OTU table of order level taxa counts
tidy_micro

A function to merge multiple OTU tables and clinical data into a "tidy" format
taxa_summary

Summarize the information
tidyeval

Tidy eval helpers
pca_3d

Create 3d PCA plots
phy

An OTU table of phylum level taxa counts
clin

A data set containing the clinical data of the subjects sequenced
cor_rocky_mtn

Create Rocky Mountain plots from taxa relative abundance correlations
alpha_div

Alpha Diversity Calculations for tidy_micro
beta_heatmap

Create heatmaps of the supplied dissimilarity matrices
bb_bars

Create stacked bar charts based on beta binomial model estimates
cor_heatmap

Create correlation heatmaps of taxa and another continuous variable
bb_mods

Fit beta binomial models to each taxa within an OTU table
cla

An OTU table of class level taxa counts
beta_div

Beta Diversity Calculations for tidy_micro