heylf

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.

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).

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).

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).

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