To calculate metabolic pathway completeness and build heatmaps from GhostKOALA output via KEGGDecoder.
This binder provides instructions and demo for the KEGGDecoder tool, which makes a metabolic heatmap. The package was developed by Ben Tully and expanded during the Speeding Up Science workshop by Jay Osvatic, Roth Conrad, Luiz Irber, and Taylor Reiter.
- Launch the binder with the button above. This will take a few minutes to load.
- Upload your ghostKOALA output to the Jupyter Notebook in your binder session with the Upload button near the top right of that page.
- Select New Python 3 Notebook from the New button next to the Upload button. This will open in a new tab.
- From this Python session execute: !KEGG-decoder --input Example_input_data.txt --output Example_output_data.tsv --vizoption interactive
- Return to the first binder session tab and click on the new function_heatmap.html file to open it in a new tab.
For more detailed instructions review documents in example_notebooks directory from within the Binder session.