PIEMMER is a python package that implement the EMMER algorithm.

EMMER, which stands for Entropy-based Method for Microbial Ecology Research, is a feature selection algorithm that reduces the number of measurements in a matrix while allowing this new matrix to retains a similar data distribution on a Principal Component Analysis (PCA) plot (see Fig. 1; view figure). We named this algorithm EMMER because it was originally developed to processing microbiota and microbiome datasets. Later, we realize this algorithm has a wider application because the shared mathematical procedure between EMMER algorithm and PCA

Fig 1. Usage of the EMMER algorithm

• Version: 1.0.6 (compared to 1.0.5: Core function remains the same. Rearrange file structure for Travis testing)
• License: BSD 3-Clause License
• Developer/Maintainer: Hao-Wei Chang (email: emmer.man42@gmail.com)
• Citation: H.-W. Chang et al., Gut microbiome contributions to altered metabolism in a pig model of undernutrition. (2021) Proc Natl Acad Sci U S A. 118, e2024446118.
  1. Main article; how to use EMMER in microbiota/microbiome studies
  2. SI Appendix; how EMMER algorithm works

Please refer to the wiki page for detailed information about download, dependency, version difference and tutorial.

conda install -c bioconda piemmer

or

pip install piemmer

Get the location of example files that were included in the package

python3

import pkg_resources
DATA_PATH = pkg_resources.resource_filename('piemmer', 'data/')
DATA_PATH

Run piemmer

cd where_your_what_to_put_the_output_files
python3 -m piemmer.harvest -g
python3 -m piemmer.bake -g

cd where_you_what_to_store_your_file
git clone https://github.com/HWChang/emmer.git

cd where_you_what_to_store_your_file/emmer
python3 -m piemmer.harvest -g
python3 -m piemmer.bake -g