/POMS_manuscript

Primary LanguageRGNU General Public License v3.0GPL-3.0

POMS_manuscript

Code used for this paper:

Gavin M. Douglas, Molly G. Hayes, Morgan G. I. Langille, Elhanan Borenstein. 2022. Integrating phylogenetic and functional data in microbiome studies. Bioinformatics 38 (22):5055-5063.

  • display_items/ - Raw image files generated by plotting scripts.

  • scripts/

    • dataset_running/ - Code for running POMS on Almeida and TARA oceans datasets.

    • display_items/ - Code for generating all figures.

    • general_processing/ - General Python scripts used for processing raw datasets

    • preprocessing/ - Code used for preprocessing specific datasets to be in format used downstream.

    • simulations/ - Code used to run metagenome-assembled genome (MAG.based; described in main text) and the simulations based on reference genomes only (ref.based; described in supplement).

    • text_stats/ - Code to parse key statistics to report in main text.

    • POMS_manuscript_functions.R - Functions used for multiple scripts.

    • alt_tool_functions.R - Functions used for running standard differential abundance tools.

Note that the key datafiles for this project are available on FigShare.