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CharitidisKP/README.md

Laptop running the CosMx-Nf pipeline

Hello, I'm Konstantinos Charitidis!

Bioinformatician in Stockholm. I work on spatial and single-cell transcriptomics, bulk RNA-seq and proteomics in autoimmune disease.

I work mostly in R and Bash, build pipelines in Nextflow, keep my code in Git and run it in Conda environments and Apptainer containers so the analyses are reproducible.

  • CosMx-Nf: Nextflow (DSL2) pipeline for CosMx spatial transcriptomics, from QC and cell typing to spatial analysis, cell-cell communication and differential expression.
  • Publication: Glycomic profiles before and after treatment for lupus nephritis, Cells 2026.

Contact

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  1. CosMx-Nf CosMx-Nf Public

    Nextflow pipeline for CosMx spatial transcriptomics

    R

  2. Glycans_Project Glycans_Project Public

    Scripts for the glycans analysis

    RMarkdown