/FuncDiv_manuscript

Code used for showcasing the FuncDiv R package

Primary LanguageRGNU General Public License v3.0GPL-3.0

FuncDiv_manuscript

Code used for showcasing the FuncDiv R package, which is now published:

Gavin M. Douglas, Sunu Kim, Morgan G. I. Langille, B. Jesse Shapiro. 2023. Efficient computation of contributional diversity metrics from microbiome data with FuncDiv. Bioinformatics 39 (1): btac809. DOI: 10.1093/bioinformatics/btac809

Repository structure:

  • data/

    • Almeida_2019_dataset/ - input data used for assessing FuncDiv resource usage.
    • random_forest/ - input and output files of random forest analysis.
    • HUMAnN3_tutorial_table/ - table taken from HUMAnN3 tutorial to use for comparison.

  • scripts/ - code used to run manuscript analyses, split up by code for random forest and resource usage analyses, and minor code for results reported in text.