https://github.com/cfrioux/cfrioux
https://github.com/cfrioux/cfrioux
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/cfrioux/cfrioux
- Owner: cfrioux
- Created: 2025-08-28T07:45:54.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2025-08-28T08:20:58.000Z (10 months ago)
- Last Synced: 2025-09-10T05:20:02.202Z (9 months ago)
- Size: 2.93 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
## Hi there 👋
My name is Clémence Frioux, welcome!
- 👩💻 I am a researcher in computational biology
- 📍 I work at Inria, a French research Institute on computer science and mathematics. I am located in Bordeaux, France
- 🧬 🦠 I am interested in the (functional) characterisation of microbial communities. I mostly work on metabolic modelling 🦠, but I also work on microbiome composition and metagenomics 🧬
- 😄 Pronouns: She/Her
- ➡️ More info on my website: [https://cfrioux.github.io]
## A few projects hosted here on Github that I want to highlight
I was not a developer in all of those projects but participated to them.
### 🧬 Mapler
Evaluation of assembly and binning quality for Hi-Fi metagenomics.
- [Repo](https://github.com/Nimauric/Mapler#)
- [Paper](https://academic.oup.com/bioinformatics/article/41/6/btaf334/8157874)
### 🧬 cvaNMF
A package for non-negative factorisation and its bi-cross validation.
- [Repo](https://github.com/apduncan/cvanmf)
### 🦠 Metage2Metabo
Pipeline dedicated to the (optional) automatic reconstruction of genome-scale metabolic network and characterising the metabolic potential and metabolic complementarity in microbial communities.
- [Repo](https://github.com/AuReMe/metage2metabo)
- [Paper](https://doi.org/10.7554/eLife.61968)
### 🦠 Metage2Metabo-postAViz
Shiny-based interface to integrate results of Metage2Metabo together with sample and taxonomic metadata, in order to compare metabolic potential across large cohorts of samples.
- [Repo](https://github.com/AuReMe/metage2metabo-postaviz)
### 🦠 MeneTools
Several tools relying on network expansion to explore metabolic networks.
- [Repo](https://github.com/cfrioux/MeneTools)
- [Paper](https://doi.org/10.1371/journal.pcbi.1006146)
### 🦠 MiSCoTo
Selection of minimal communities ensuring the reachability of target metabolites, using a collection of metabolic networks
- [Repo](https://github.com/cfrioux/miscoto/tree/main)
- [Paper](https://academic.oup.com/bioinformatics/article/34/17/i934/5093211)
### 🦠 Seed2LP
Inference of seeds (environmental composition) from metabolic networks, using network expansion and flux balance analysis. Can be used for individual populations and microbial communities.
- [Repo](https://github.com/bioasp/seed2lp)
- [Paper for individual populations](https://academic.oup.com/bioinformatics/article/41/4/btaf140/)
- [Paper for microbial communities](https://link.springer.com/chapter/10.1007/978-3-032-01436-8_20)
### 🦠 Meneco
Gap-filling of metabolic networks.
- [Repo](https://github.com/cfrioux/meneco)
- [Paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005276)
### 🦠 AuCoMe
Automatic reconstruction and comparison of metabolic networks.
- [Repo](https://github.com/AuReMe/aucome)
- [Paper](https://doi.org/10.1101/gr.277056.122)
### 🦠 mpwt
Python wrapper for Pathway Tools (reconstruction of metabolic networks).
- [Repo](https://github.com/AuReMe/mpwt/tree/e95165878dcaa422ef4cef96d75489fc7d0ad677)
- [Paper](https://doi.org/10.7554/eLife.61968)