Microbiome Toolbox
Project description
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
microbiome-toolbox-0.0.3.tar.gz
(36.9 kB
view hashes)
Built Distribution
Close
Hashes for microbiome_toolbox-0.0.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ed1a6b625e6a067e1b07aba84c5e580b5e2f6c817a2b872d7994b3db31c15b78 |
|
MD5 | 523f64c9c6fe8d2715cbe2eb7aa5b23a |
|
BLAKE2b-256 | 7fe4ebc1cf1a7f3a43d7a755c1072276f5140e95186b9c4ab18e5f8be9dd9f41 |