Weight loss after a lifestyle intervention

Data and scripts for the weight loss project funded by the ISB Innovator Award.

Organization

root
    > data     # raw and intermediate data
    > figures  # generated figures
    > *.rmd    # Notebooks for the analyses

Setup

You will require a working Rstudio installation to run the notebooks.

Open Rstudio switch to the "console" tab and enter the following:

source("install.R")

This will install all requirements to run the basic analyses.

Steps

Here are the analyses we ran and the rendered outputs:

1. Cohort design from the Arivale data set notebook | output
2. Basic trajectories of the cohort notebook | output
3. Analysis of baseline measures in the cohort notebook | output
4. Analysis of the SRM data for 25 people subcohort notebook | output
5. Associations between metabolome and weight loss notebook | output
6. Associations between proteome and weight loss notebook | output
7. Associations between 16S genus abundances and weight loss notebook | output
8. Associations between food consumption frequencies and weight loss notebook | output
9. Associations between species abundances and weight loss notebook | output
10. Associations between gene clusters and weight loss notebook | output
11. Analysis of bacterial contig replication rates notebook | output
12. SRA submission notebook | output