Hi! I am Florian - Nice to meet you 👋

💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.

🔥 Key Projects

Tools

• A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets: StoatyDive.
• Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects: LiMetrack.
• There are more private projects (please ask me about them).

Workflows

• Nextlfow Xenium data processing pipeline: nf-core/spatialxe.
• Galaxy spatial omics gene pane design workflow: Spatial Omics Marker gene detection workflow.
• A webserver to process, analyse and visualise CLIP-Seq data: Galaxy CLIP Explorer.
• Galaxy ATAC-Seq data processing workflow: ATAC-Seq workflow, together with the Galaxy ATAC-Seq training material ATAC-Seq data analysis.
• Galaxy CUT&RUN data processing worfklow: CUT&RUN workflow, together with the Galaxy CUT&RUN training material CUT&RUN data analysis.
• There are more private projects (please ask me about them).

Other Projects that I am supporting

• A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis: nf-core/variantbenchmarking.
• Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data: nf-core/scrnaseq.
• A flexible framework for applying spatially aware clustering methods: SACCELERATOR.
• Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others: nf-core/mcmicro.
• There are more private projects (please ask me about them).

🎓 Scientific Interests:

• Image-based spatial transcriptomics
  • Artefact detection
  • Quality control
  • Noise estimation
  • Standard data processing
• Single cell multiomics
  • Standardized data processing
  • Demultiplexing
  • Quality control
  • Artefact detection
• Bioinformatics pipelining
  • Nextflow, Galaxy, Snakemake
  • Scaling
  • Deploying workflows
  • resource and parameter optimization

🌱 I’m also exploring:

• GPU-accelerated data processing
• Manifolds

📭 How to reach me:

• Email: florian.heyl@dkfz-heidelberg.de
• LinkedIn: https://www.linkedin.com/in/florian-heyl/

📊 GitHub Stats: