This repository provides code to reproduce the major analyses of the unpublished manuscript titled "Blood RNA Signatures Predict Recent Tuberculosis Exposure in Mice, Macaques and Humans". The major analyses of the paper can be reproduced by running the jupyter notebook "Time Since Infection_Submission_Streamlinedcode.ipynb".
This code was developed and used in a linux environment and has not been modified to aid in running with other platforms.
This software is available under the MIT license. However, the script utils_immunoStates.R contains code that is copied from the MetaIntegrator R package, and thus this script is under an LGPL license.
Installation (for running the provided jupyter notebook with R; alternatively, can simply view the provided .html)
- Install anaconda (a local installation manager and python distribution)[https://docs.anaconda.com/anaconda/install/], and create a new conda environment
$ conda create --name TB python=3.6.3
$ conda activate TB
- Install r-essentials with mro base R version 3.4.3 (the R version used in this analysis)
conda install -c r mro-base=3.4.3 r-essentials
- Install or make sure the following python packages are installed:
- Pandas
- jupyter
- jupyter notebook extensions (for easy browsing of the analysis notebook)
conda install -c conda-forge pandas jupyter jupyter_contrib_nbextensions
- Open R from command-line and run IRkernel so that jupyter notebook can see the R installation
R
> IRkernel::installspec()
- Alternatively, use the provided env_list.txt and environment.yml files to reproduce the environment in which this analysis was performed. However, many packages in this environment are not necessary.
- Run the provided download scripts from the base repository directory to download required public data for the analyses.
bash download_macaque_human_data.sh
- Reproduce the major analyses of the paper by running the jupyter notebook "Time Since Infection_Submission_Streamlinedcode.ipynb" and following the steps it describes.