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tstohn/README.md

Me

I am building fast, memory-efficient software to study signaling on the single-cell level. Leveraging novel single-cell datasets like sequencing based single-cell protein measurement technologies I am working on scalable tools to decode cellular signaling networks. Therefore, i develop solutions from the raw data processing to methods to infer singlaing networks.

I develop fast, memory-efficient, and scalable software solutions for single-cell data analysis, with a strong focus on extracting meaningful biological insights from complex datasets. My current research centers on (phospho)protein data, where I study correlation patterns at the single-cell level to infer signaling networks. My work spans the full analytical pipeline, from raw data processing and normalization to downstream network analysis.

I am proficient in C++, R, and Python, and particularly interested in performance-oriented computing and scalable algorithm design for large biological datasets. I am currently a PhD student based in Leiden, completing my doctorate at the Netherlands Cancer Institute (NKI) in collaboration with VU Amsterdam. I previously studied Biotechnology at TU Berlin and Bioinformatics at the University of Hamburg.

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  1. ESGI ESGI Public

    ESGI can be used to demultiplex any barcoded single-cell sequencing data and to create the single-cell * feature matrix. ESGI gives the user a lot of flexibility in the patterns to demultiplex/ the…

    C++ 1 1

  2. LoCo LoCo Public

    LoCo: local correlation analysis searches for local correlation patterns in single-cell data that change smoothly across the single-cell graph.

    C++

  3. Analysis-ESGI Analysis-ESGI Public

    This repository contains all the script for the Paper of the method ESGI.

    Jupyter Notebook

  4. scmra_analysis scmra_analysis Public

    This repository contains all the code for the scMRA/scCNR paper 'Reconstructing and comparing signal transduction networks from single cell protein quantification data'.

    Jupyter Notebook

  5. ibivu/scmra ibivu/scmra Public

    scMRA python module

    Python 3