micro_ecol
Scripts used in the analysis of amplicon microbiota data
clean_repFasta_FAST.py
Renames fasta sequences output from mothur from automatically generated name to OTU #
Pairwise_adonis
Functions to run pairwise PERMANOVAs with multiple comparison (fdr) correction across all levels variables of interest across beta-diversity measures. Adapted from Pedro Martinez Arbizu (https://www.researchgate.net/post/How_can_I_do_PerMANOVA_pairwise_contrasts_in_R).
- Multiple variables of interest allowed.
- Bray-Curtis, Jaccard, or UniFrac allowed.
- Stratification of model allowed with strata option.
- Output saved to object in R environment.
pairwise_permdisp.R
Permutational tests of beta-dispersion (PERMDISP) across multiple variables of interest and pairwise with TukeyHSD. Multiple variables of interest allowed. Bray-Curtis or Jaccard only.
R_krusk.R
Automates Kruskal-Wallis test execution on OTUs of interest as determined by simper_pretty.R. See https://github.com/asteinberger9 for up to date version
simper_pretty.R
Automates SIMAPERA execution for comparisons OTUs across variables of interest. See https://github.com/asteinberger9 for up to date version