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address #53, update dependencies of miscoto and menetools in README
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cfrioux committed Jan 5, 2024
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Expand Up @@ -69,8 +69,8 @@ pip install -r requirements.txt --no-cache-dir
In particular, m2m relies on:
* [mpwt](https://github.com/AuReMe/mpwt) to automatize metabolic network reconstruction with Pathway Tools
* [padmet](https://github.com/AuReMe/padmet) to manage metabolic networks
* [menetools](https://github.com/cfrioux/MeneTools) to analyze individual metabolic capabilities using logic programming
* [miscoto](https://github.com/cfrioux/miscoto) to analyze collective metabolic capabilities and select communities within microbiota using logic programming
* [menetools](https://github.com/cfrioux/MeneTools) to analyze individual metabolic capabilities using logic programming. **Requires MeneTools > 3.4**
* [miscoto](https://github.com/cfrioux/miscoto) to analyze collective metabolic capabilities and select communities within microbiota using logic programming. **Requires MiSCoTo > 3.2**

Also, m2m_analysis relies on other packages:
* [networkx](https://github.com/networkx/networkx) to create graph from miscoto results
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