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 |