Analysis and Visualization Tools for Microbial Community Data


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Documentation for package ‘theseus’ version 0.1.0

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cohort_relabund Creates a relative abundance cohort plot
constord Plots constrained ordination results
envtoverlay Environmental variable fitting to unconstrained ordination diagrams
prev Create prevalence vs abundance plot
pstoveg_otu converts the otu_table slot of a phyloseq object to a vegan-compatible matrix
pstoveg_sample Converts sample_data slot of a phyloseq object to vegan-compatible matrix
pstoveg_sd converts the sam_data slot of a phyloseq object to a vegan-compatible matrix
qualcontour Create read quality color contour plots
sigtab Differential abundance data
sigtab.2vs3 Differential abundance data
WWTP_Impact Freshwater stream microbiome data