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mulbagalamaq/README.md

Hello!
I’m Aymen (pronounced aye-men), I am a Bioinformatician with experience in high-dimensional biological data analysis (single-cell RNA-seq, CRISPR-edited NGS, CHIP-seq, ATAC-seq and CITE-seq).

I have experience developing reproducible pipelines (Nextflow, Snakemake), interactive tools/dashboards (R Shiny, Streamlit), and leveraging cloud platforms (AWS EC2, S3, TERRA) for scalable analyses. Currently learning to integrate multi-omics data and fine-tune ML genomic models.

Python R Bash Script Docker Nextflow Git Jupyter Notebook AWS Linux

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  1. NK-Cell-Classifier NK-Cell-Classifier Public

    GPU-accelerated single-cell RNA-seq workflow for exploring NK cell differentiation using CITE-seq data from Foltz et al. 2024 (Science Immunology).

    Jupyter Notebook

  2. collaborativebioinformatics/BioGraphRAG collaborativebioinformatics/BioGraphRAG Public

    Implement a system to use GNN and/or LLM to use knowledge graphs to integrate literature with knowledge graphs made from large public datasets (CIVIC, TCGA, CPTAC)

    Python 8 1

  3. GlycoEnzyme-Expression-Atlas GlycoEnzyme-Expression-Atlas Public

    Forked from BioITHackathons/GlycoEnzyme-Expression-Atlas

    BIO IT hackathon 2025

    R

  4. GWAS-Analysis GWAS-Analysis Public

    GWAS Analysis of Early onset Pancreatic Cancer

    Jupyter Notebook

  5. ATAC_seq ATAC_seq Public

    Integration of multi-omics data to study gene regulation and cell differentiation.

    HTML

  6. stack-perturb-data stack-perturb-data Public

    Exploratory analysis using Arc Institute's Stack foundation model

    Jupyter Notebook