Tianyi_microbiome

This repository contains the final code, count table, metadata, and precomputed data files for "The gut microbiota of healthy aged Chinese is similar to the healthy young".
tianyi_results.Rnw builds cleanlytianyi_supplement.Rnw builds cleanly
tianyi_results.Rnw file contains the knitr document and minimal code for figures 1-3 of the papertianyi_supplement.Rnw file contians the code and figures for the supplement
chunk/ contains actual R commands used for all figures and analyses. These are referenced in the results and supplement documents
data/ contains the raw (count tables, metadata) and precomputed data for the figures
figure/ contains the figures only
to build the documents, download this entire repository, then in a terminal on a UNIX type machine run:
./build_results.sh
and then
./build_supplement.sh