CD1bGMM

This repo reproduces analysis and plots for our paper:

A diverse lipid antigen-specific T cell receptor repertoire is clonally expanded during active tuberculosis. DeWitt WS, Yu KKQ, Wilburn DB, Sherwood A, Vignali M, Day CL, Scriba TJ, Robins HS, Swanson WJ, Emerson RO, Bradley PH, Seshadri C. Journal of Immunology June 18, 2018, ji1800186; DOI: https://doi.org/10.4049/jimmunol.1800186.

Data: http://dx.doi.org/doi:10.21417/B7QG66

Dependencies

• scons
• Python 2.7+/3.5+, with modules:
  • scipy
  • matplotlib
  • seaborn
  • pandas
  • biopython
  • scikit-learn
• TCRdist is a submodule, so clone recursively when you clone this repo with
  git clone --recursive https://github.com/seshadrilab/CD1bGMM.git,
  or if you've already cloned this repo, run
  git submodule update --init --recursive to add the TCRdist submodule.

For installing scons, and python dependencies, conda is recommended:

conda install scons scipy matplotlib seaborn pandas biopython scikit-learn

Alternatively, a linux spec file for a python2 environment is included (spec-file.txt), which may be used to create a conda environment containing all necessary dependencies. To create an environment called myenv, execute
conda create --name myenv --file spec-file.txt,
then activate the environment with
source activate myenv.

Generate results

Simply issue the command scons. Necessary data will be downloaded, and plot output will be created in a directory named output.