human_metagenomes_analysis

A Metagenomic Meta-Analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome

File descriptions:

make_circos_karyotype.R

Code for creating the karyotype used to make the circos plot in the manuscript

make_dataframes_for_cplm.R

Used to produce a dataframe for each kegg object in each disease with the KEGG object abundance and sample disease status. Used for running regression models.

manuscript_figures.R

Code for creating the figures in the manuscript (except the circos plot)

metagenome_analysis_functions.R

Functions created for this project, this file is sourced in most of the other scripts.

ms_review.R

This file contains the code for the analyses described in Supplemental text 1 of the manuscript.

run_model.R

The code for running CPGLM on the dataframes created with the make_dataframes_for_cplm.R script.