microbiome-toolbox 0.0.2

Microbiome Toolbox

Microbiome Toolbox

Website

Microbiome Toolbox

Install your package from the real PyPI using python3 -m pip install [your-package].

Note:

# 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