Science Score: 13.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Repository
QIIME2 plugin for `ili
Basic Info
Statistics
- Stars: 1
- Watchers: 6
- Forks: 2
- Open Issues: 4
- Releases: 0
Topics
Metadata Files
README.md
QIIME 2 `ili plugin
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
This plugin is wrapping `ili, for more information, see https://github.com/MolecularCartography/ili.
Installation
To install q2-ili you need a working QIIME 2 installation. After you have
installed QIIME 2, clone and install q2-ili by running these commands:
bash
git clone --recurse-submodules https://github.com/biocore/q2-ili.git && cd q2-ili
pip install .
qiime dev refresh-cache
Troubleshooting installation
If the git command above results in an error like the following:
bash
error: Server does not allow request for unadvertised object...
you may need to update the version of git that is installed on your system. You can download the latest version of git here.
Requirements
In order to use this plugin, you need a 3D model in STL format and a mapping
between your samples and their coordinate locations in the model. To do this
your QIIME 2 metadata file needs to include three columns labeled x, y and
z. For more information see `ili's
documentation.
Example
To exemplify how to use q2-ili, we will use the data from Bouslimani et al.
2015. The metabolomic features will
be colored in the model according to the site where they were collected from.
The data for this example is included in the example-data directory of the
repository you cloned above.
First we need to import the model as a QIIME2 artifact. The type Model is
installed in QIIME 2 along with this plugin, hence we can run the following
command:
bash
qiime tools import \
--type Model \
--input-path example-data/model.stl \
--output-path model.qza
Next, we generate the visualization using the model and the numeric data that we have in the metadata file:
bash
qiime ili plot \
--i-model model.qza \
--m-metadata-file example-data/metadata.tsv \
--o-visualization visualization.qzv
Lastly, you can visualize and interact with this model using q2view.
Owner
- Name: biocore
- Login: biocore
- Kind: organization
- Location: Cyberspace
- Website: http://biocore.github.io/
- Repositories: 76
- Profile: https://github.com/biocore
Collaboratively developed bioinformatics software.
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 8
- Total pull requests: 9
- Average time to close issues: N/A
- Average time to close pull requests: 4 minutes
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ElDeveloper (4)
Pull Request Authors
- ElDeveloper (5)
- gregcaporaso (1)