Analytics for salt & microbiome

File structure

data/ has:

• rdp_g.counts: an OTU table showing the counts of the RDP genus-level OTUs
• rdp_g.melt: a "melted" version of the OTU table including sample data

analysis/ has subfolders corresponding to different analyses shown in the paper:

• ordination-permanova has the ordination plot and PERMANOVA analyses (Figures S3A, S3B).
• enrichment has the analysis about which taxa were enriched in the two treatments. It has one file enrichment.R that performs the analysis.
• tree has the phylogenetic tree and the scripts used to decorate the tree with the enrichment information (Figure S3D).
• classifier has the classifier analysis (Figures 1A, 1B).
• timeseries has the analysis about the dynamics of specific taxa (Figure 1C). It has one file timeseries-plots.R that uses the OTU table to generate timeseries plots for select OTUs.

Author

• Scott Olesen (swo [at] alum [dot] mit [dot] edu)