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tidyMicro

The goal of tidyMicro is to provide a cohesive pipeline for microbiome data analysis and visualization.

Installation

You can install the released version of tidyMicro from CRAN with:

install.packages("tidyMicro")

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 PCA plots

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Version

Install

install.packages('tidyMicro')

Monthly Downloads

8

Version

1.47

License

GPL-3

Maintainer

Charlie Carpenter

Last Published

September 13th, 2020

Functions in tidyMicro (1.47)

bpd_ord

An OTU table of order level taxa counts study
micro_PERMANOVA

A function to run PERMANOVA on tidi_micro data sets
bpd_phy

An OTU table of phylum level taxa counts study
micro_alpha_reg

Linear regression on alpha diversities within a micro_set
ra_bars

Function to make stacked bar charts of taxa relative abundance
taxa_boxplot

Function to make boxplots of taxa counts or relative abundance
micro_pca

Calculate and plot principle components
nb_bars

Create stacked bar charts based on negative binomial model estimates
micro_chisq

Run Chi-Squared tests for each taxa
micro_rank_sum

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

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

An OTU table of family level taxa counts from BPD1 study
bpd_clin

A data set containing the clinical data of the subjects sequenced for BPD1 study
bb_bars

Create stacked bar charts based on beta binomial model estimates
pca_3d

Create 3d PCA plots
alpha_div

Alpha Diversity Calculations for tidy_micro
micro_forest

Create forest plots from negative binomial taxa models
cor_heatmap

Create correlation heatmaps of taxa and another continuous variable
cor_rocky_mtn

Create Rocky Mountain plots from taxa relative abundance correlations
tidy_micro

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

Pipe operator
otu_filter

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

Create Rocky Mountain plots from negative binomial taxa models
tidyeval

Tidy eval helpers
beta_heatmap

Create heatmaps of the supplied dissimilarity matrices
mrsa_clin

A data set containing the clinical data of the subjects sequenced for MRSA study
bb_mods

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

An OTU table of class level taxa counts from a BPD1 study
three_mode

Create Three Mode PCA and PCoA plots
taxa_summary

Summarize the information
beta_div

Beta Diversity Calculations for tidy_micro
micro_otu

Extract OTU table from tidyMicro set
micro_heatmap

Create heatmaps of estiamted coefficients from negative binomial models
mrsa_gen

An OTU table of genus level taxa counts from a MRSA study