{"id":30582251,"url":"https://github.com/cfrioux/cfrioux","last_synced_at":"2026-02-13T17:04:06.318Z","repository":{"id":312056843,"uuid":"1046109668","full_name":"cfrioux/cfrioux","owner":"cfrioux","description":null,"archived":false,"fork":false,"pushed_at":"2025-08-28T08:20:58.000Z","size":3,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-09-10T05:20:02.202Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cfrioux.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2025-08-28T07:45:54.000Z","updated_at":"2025-08-28T08:21:02.000Z","dependencies_parsed_at":"2025-08-28T15:34:50.275Z","dependency_job_id":"93c259f9-9634-4b6b-8a75-bffd3f1b3931","html_url":"https://github.com/cfrioux/cfrioux","commit_stats":null,"previous_names":["cfrioux/cfrioux"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/cfrioux/cfrioux","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cfrioux%2Fcfrioux","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cfrioux%2Fcfrioux/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cfrioux%2Fcfrioux/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cfrioux%2Fcfrioux/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cfrioux","download_url":"https://codeload.github.com/cfrioux/cfrioux/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cfrioux%2Fcfrioux/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29412670,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-13T06:24:03.484Z","status":"ssl_error","status_checked_at":"2026-02-13T06:23:12.830Z","response_time":78,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-08-29T07:37:46.335Z","updated_at":"2026-02-13T17:04:06.304Z","avatar_url":"https://github.com/cfrioux.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"## Hi there 👋\n\nMy name is Clémence Frioux, welcome!\n\n- 👩‍💻 I am a researcher in computational biology\n- 📍 I work at Inria, a French research Institute on computer science and mathematics. I am located in Bordeaux, France\n- 🧬 🦠 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 🧬\n- 😄 Pronouns: She/Her\n- ➡️ More info on my website: [https://cfrioux.github.io]\n\n## A few projects hosted here on Github that I want to highlight\nI was not a developer in all of those projects but participated to them. \n\n### 🧬 Mapler\n\nEvaluation of assembly and binning quality for Hi-Fi metagenomics.\n\n- [Repo](https://github.com/Nimauric/Mapler#)\n- [Paper](https://academic.oup.com/bioinformatics/article/41/6/btaf334/8157874)\n\n### 🧬 cvaNMF\n\nA package for non-negative factorisation and its bi-cross validation. \n\n- [Repo](https://github.com/apduncan/cvanmf)\n\u003c!-- [Paper]() --\u003e\n\n### 🦠 Metage2Metabo\n\nPipeline dedicated to the (optional) automatic reconstruction of genome-scale metabolic network and characterising the metabolic potential and metabolic complementarity in microbial communities. \n\n- [Repo](https://github.com/AuReMe/metage2metabo)\n- [Paper](https://doi.org/10.7554/eLife.61968)\n\n### 🦠 Metage2Metabo-postAViz\n\nShiny-based interface to integrate results of Metage2Metabo together with sample and taxonomic metadata, in order to compare metabolic potential across large cohorts of samples. \n\n- [Repo](https://github.com/AuReMe/metage2metabo-postaviz)\n\n\n### 🦠 MeneTools\n\nSeveral tools relying on network expansion to explore metabolic networks.\n\n- [Repo](https://github.com/cfrioux/MeneTools)\n- [Paper](https://doi.org/10.1371/journal.pcbi.1006146)\n\n### 🦠 MiSCoTo\n\nSelection of minimal communities ensuring the reachability of target metabolites, using a collection of metabolic networks\n\n- [Repo](https://github.com/cfrioux/miscoto/tree/main)\n- [Paper](https://academic.oup.com/bioinformatics/article/34/17/i934/5093211)\n\n### 🦠 Seed2LP\n\nInference of seeds (environmental composition) from metabolic networks, using network expansion and flux balance analysis. Can be used for individual populations and microbial communities.\n\n- [Repo](https://github.com/bioasp/seed2lp)\n- [Paper for individual populations](https://academic.oup.com/bioinformatics/article/41/4/btaf140/)\n- [Paper for microbial communities](https://link.springer.com/chapter/10.1007/978-3-032-01436-8_20)\n\n### 🦠 Meneco\n\nGap-filling of metabolic networks.\n\n- [Repo](https://github.com/cfrioux/meneco)\n- [Paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005276)\n\n### 🦠 AuCoMe\n\nAutomatic reconstruction and comparison of metabolic networks. \n\n- [Repo](https://github.com/AuReMe/aucome)\n- [Paper](https://doi.org/10.1101/gr.277056.122)\n\n### 🦠 mpwt\n\nPython wrapper for Pathway Tools (reconstruction of metabolic networks).\n\n- [Repo](https://github.com/AuReMe/mpwt/tree/e95165878dcaa422ef4cef96d75489fc7d0ad677)\n- [Paper](https://doi.org/10.7554/eLife.61968)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcfrioux%2Fcfrioux","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcfrioux%2Fcfrioux","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcfrioux%2Fcfrioux/lists"}