This repository contains a jupyter notebook that reads in the raw data from the CRyPTIC project and reproduces the vast majority of the Tables and Figures in the below preprint.
Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis The CRyPTIC Consortium medRxiv preprint doi:10.1101/2021.02.24.21252386
The easiest way by far is to click the launch binder button at the top of this document. This will open a MyBinder session which will install all the required software on a remote container (this can take a few minutes) and furnish you the notebook in browser. You can then run each cell in turn, or add new cells and write your own Python/Pandas code to interrogate the data and analysis. The graphs are, however, not written to the graphs/ folder when using MyBinder. For that you need to install it locally.
This requires a little more knowledge, but if you have any Python experience should be familiar. In brief, in a terminal
$ git clone git@github.com:fowler-lab/cryptic-ecoffs.git
$ cd cryptic-ecoffs/
$ pip install .
$ jupyter-lab reproduce-tables-and-figures.ipynb
The last command should open a window in your default browser and load the notebook. Again, like with MyBinder you can then step through and run all the cells. All the graphs are written as PDF files to graphs/ and are identical to the ones in the manuscript.
This README will be updated when the manuscript is published in a peer-reviewed journal.