BabyGut16S

Code used for the analysis of 16S data from infant gut samples, published by Beller et al. (insert ref).

Data

Data files include:

• metadata file (metadata information per sample)
• abundance file (read counts per ASV, per taxon, after preprocessing as described in the paper)
• taxonomy file (per ASV, the taxonomic information)

And a seperate folder containing the results from projecting the infant samples to adult samples from the FGFP dataset.

Code

The code is written in R, in a Markdown file that can be converted to pdf (or html) using knitr. Don't forget to change the working directory (Workdir variable) at line 22.

Output

All figures are saved in an automatically created output directory. An example of how it normally looks is shown.