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💻 📊 Analyses to recreate the results in the manuscript "XXX" by XXX et al. 2018 in XXX. The analyses are setup to run in a Linux environment and are separated into several R Markdown files.

Create environments

Setup the same environments used to analyze the data by cloning the GitHub repository and running the setup.sh script as follows:

Render R Markdown files

Adhere to the delineated order as succeeding R Markdown files depend on previous results. X11 forwarding may be needed if working remotely.

1. data_curation.Rmd
2. fasta_demux_qc.Rmd
3. otu_tables.Rmd
4. tax_align_bact.Rmd
5. tax_align_arch.Rmd
6. bact_rarefaction_alpha_diversity.Rmd
7. arch_rarefaction_alpha_diversity.Rmd
8. bact_taxa_beta_diversity.Rmd
9. arch_taxa_beta_diversity.Rmd
10. discovery_samples.Rmd
11. bact_differential_otus.Rmd
12. arch_differential_otus.Rmd
13. bact_forward_regression.Rmd
14. arch_forward_regression.Rmd

To render an R markdown file:

  • change to the 2018_methane directory
  • source anaconda/bin/activate bioinfo
  • anaconda/envs/stats/bin/Rscript -e "rmarkdown::render('[1-14]')" (replace [1-14] with the name of the markdown file)