A Pipeline for Microbiome Analysis and Visualization


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Documentation for package ‘tidyMicro’ version 1.47

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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
bpd_cla An OTU table of class level taxa counts from a BPD1 study
bpd_clin A data set containing the clinical data of the subjects sequenced for BPD1 study
bpd_fam An OTU table of family level taxa counts from BPD1 study
bpd_ord An OTU table of order level taxa counts study
bpd_phy An OTU table of phylum level taxa counts study
cor_heatmap Create correlation heatmaps of taxa and another continuous variable
cor_rocky_mtn Create Rocky Mountain plots from taxa relative abundance correlations
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_otu Extract OTU table from tidyMicro set
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
mrsa_clin A data set containing the clinical data of the subjects sequenced for MRSA study
mrsa_gen An OTU table of genus level taxa counts from a MRSA study
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
otu_filter A function to aggregate low prevalence, abundance, or unwanted taxa together
pca_3d Create 3d PCA plots
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