Guillaume Charbonnier
Freelance Bioinformatician
Provence-Alpes-Côte d'Azur, France
Summary
🤩
Rockstar🎓
Top SchoolGuillaume Charbonnier is a freelance bioinformatician with nine years of experience turning high-throughput sequencing data into reproducible, publication-ready results, supporting projects from experimental design to analysis, workflow development, consulting and training. He combines strong computational fluency (Linux, Bash, R/Bioconductor, Python, Snakemake, Conda, Docker, Git) with a research background at INSERM and a PhD in bioinformatics/genomics, enabling scalable, well-documented pipelines across RNA-Seq, ChIP-Seq, ATAC-Seq and bisulfite-seq. As an active contributor to the bioconda-recipes ecosystem he has automated builds and resolved dependency issues for widely used bioinformatics tools, demonstrating attention to reproducibility and distribution. Comfortable bridging academic and industry contexts (AstraZeneca placement, multiple internships), he also delivers training and practical workflows that make complex analyses accessible to collaborators. Notably, his profile blends formal project management training with deep technical and domain expertise, helping teams move from raw data to publishable insights.
9 years of coding experience
3 years of employment as a software developer
Master's degree, Management de projet, Master's degree, Management de projet at KEDGE Business SchoolMaster's degree, Biological Engineering, Master's degree, Biological Engineering at Aix-Marseille University - Polytech MarseilleMaster's degree, Bioinformatics, Structural Biochemistry and Genomics, Master's degree, Bioinformatics, Structural Biochemistry and Genomics at Aix-Marseille UniversityClasse Préparatoire BCPST, Biologie, Chimie, Physique et Sciences de la Terre, Classe Préparatoire BCPST, Biologie, Chimie, Physique et Sciences de la Terre at Lycée Masséna
English, Italian, French
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (8)
bioinformatics10
bash10
conda10
package-management10
build-automation9
python9
docker8
dockers8
Programming languages (10)
Github contributions (5)
bioconda/bioconda-recipes
Jan 2017 - May 2022
Conda recipes for the bioconda channel.
Role in this project:
Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:22 commits, 34 PRs, 27 pushes in 5 years 4 months
Contributions summary:Guillaume contributed to the bioconda-recipes repository by creating and modifying recipes for various bioinformatics tools. They added new recipes for tools like `hmmlearn`, `pygtftk`, `jvarkit-bam2wig`, `jvarkit-bam2svg`, and updated existing ones. These changes involved adjusting build scripts, test configurations, and fixing issues related to dependencies and versions to ensure compatibility within the bioconda environment. The user also maintained the build process, modifying files and scripts to adapt to changing dependencies.
recipescondabiocondabioinformaticspackage-management
guillaumecharbonnier/mw-lib
Jul 2019 - Feb 2025
Metaworkflow library of generalised Snakemake rules
Contributions:1 release, 2 reviews, 29 PRs in 5 years 7 months
snakemakerulesworkflow
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