Idenifies and removes sub OTUs which grow under room temperature storage conditions.
Download the repository from GitHub, and navigate into that directory. The repository can be installed by running the following commands in the linux terminal.
conda create -n bloom pip python=3 numpy jupyter seaborn matplotlib=1.5.1 statsmodels
source activate bloom
pip install scikit-bio
pip install emperor --pre
pip install -e .
All analysis notebooks can be initialized by running the command jupyter notebook from the terminal.
- ag_alpha_diversity.ipynb: Evaluates the effect of the identified bloom sequences on the difference in alpha diversity in the American Gut Project data
- bloom_example Demonstrates the application of the bloom filter to sample data
- effect-of-blooms-on-bray-curtis-distance.ipynb: Evaluates changes in beta diversity between samples shipped through local post and samples that were frozen shortly after collection.
- identify-candidate-blooms.ipynb: Identifies the bloom sequences in the American Gut data based on comparison with storage studies and fresh frozen samples.