This repo contains the code used for the analyses that support findings of the paper entitled: "Genetic remodeling of soil diazotrophs enables partial replacement of synthetic nitrogen fertilizer with biological nitrogen fixation in maize"
To run the code, you will need to recreate the analysis environment using the environment.yml
file provided. To do this you will need to have conda
installed. For detail instructions on how to install, visit the conda website.
Once conda is installed, the environment can be configured using:
conda env create -f environment.yml
Now activate the environment.
conda activate moa_paper
The analysis is organized in three main sections. Each section includes datasets, analysis notebooks and output figures or tables:
1_LAB_ASSAYS
includes analysis of in-vitro and in-planta assays2_FIELD_TRIALS
includes analysis of d15N natural abundance and 15N enrichment-dilution field experiments, as well as N fertilizer response trials at Purdue University.3_ONFARM_TRIALS
includes analysis of plant N status and grain yields from the on-farm field trials
Within each folder, specific analyses are contained in the jupyter notebooks (.ipynb
). These have been exported as .html
for preview. If you want to run the code, you will need to launch jupyter
. We recommend VS Code's jupyter notebooks integration for ease of use. Notebooks are sequentially numbered according to the order they are meant to be run.
For any questions, please contact Rafael Martinez-Feria (rmartinez-feria@pivotbio.com)