Metadata-Version: 2.1
Name: microbiome-toolbox
Version: 0.0.4
Summary: Microbiome Toolbox
Home-page: UNKNOWN
Author: Jelena Banjac
Author-email: msjelenabanjac@gmail.com
License: UNKNOWN
Description: <div align="center">
          <p>
          <img src="https://image.freepik.com/free-vector/pathogen-microorganisms-set_74855-5909.jpg" alt="https://www.freepik.com/pch-vector" width="270" />
          </p>
          <p>
            <a href="">
              <img alt="First release" src="https://img.shields.io/badge/release-v1.0-brightgreen.svg" />
            </a>
          </p>
        
          <p>
            <strong>Microbiome Toolbox</strong>
          </p>
          
          <p>
            <a href="https://microbiome-toolbox.herokuapp.com">
              Website
            </a>
          </p>
        </div>
        
        
        # Microbiome Toolbox
        
        
        
        Install your package from the real PyPI using python3 -m pip install [your-package].
        
        **Note:**
        ```bash
        # building package
        #python setup.py sdist bdist_wheel
        python setup.py develop
        ```
        
        ## Songbird
        
        ```
        source activate microbiome
        
        # These instructions are identical to the Linux (64-bit) instructions (or download manually from the link)
        wget https://data.qiime2.org/distro/core/qiime2-2020.11-py36-linux-conda.yml
        conda env create -n qiime2-2020.11 --file qiime2-2020.11-py36-linux-conda.yml
        # OPTIONAL CLEANUP
        rm qiime2-2020.11-py36-linux-conda.yml
        
        pip install songbird==0.8.2
        
        songbird multinomial \
        	--input-biom ../../temp2/data/oral-collapsed-table.biom \
        	--metadata-file ../../temp2/data/oral_trimmed_metadata.txt \
        	--formula "C(label, Treatment('other'))" \
        	--epochs 10000 \
        	--differential-prior 0.5 \
        	--training-column Test \
        	--summary-interval 1 \
        	--summary-dir results
        ```
        
        ```
        songbird multinomial --input-biom ../../temp2/data/oral-collapsed-table.biom --metadata-file ../../temp2/data/oral_trimmed_metadata.txt --formula "C(label, Treatment('other'))" --epochs 10000 --differential-prior 0.5 --training-column Test --summary-interval 1 --summary-dir results
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
