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Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

Achievements

Achievement: Pair ExtraordinaireAchievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault ContributorAchievement: Pull Sharkx2

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Claptar/README.md

👋 About me

I'm Aljes, a bioinformatician / data scientist based in Cambridge, UK.

I work at the intersection of single-cell genomics, spatial transcriptomics, and reproducible computational workflows. My main focus is building analysis pipelines and developer-friendly tools for large-scale omics data — from raw sequencing outputs and quality control to downstream biological interpretation.

I’m especially interested in:

  • 🧬 Single-cell & spatial omics: scRNA-seq, scATAC-seq, multiome, Xenium, Visium
  • ⚙️ Workflow engineering: Nextflow, Docker/Singularity, scalable pipeline design
  • 🐍 Python tooling for bioinformatics: CLIs, reusable utilities, AnnData / .h5ad workflows
  • 🧠 Representation learning for genomics: embedding models for chromatin accessibility and biological structure
  • 🧱 Software design & architecture: design patterns, maintainable code, and clean abstractions
  • 📊 Data analysis & visualization: Scanpy, Squidpy, scVI, pandas, NumPy, matplotlib, Plotly

🔬 Featured work

  • spatialMPFC — analysis of human-specific features of prefrontal cortex spatial organization using spatial transcriptomics
  • nf-atac — pipeline for processing single-cell ATAC-seq data with pyCisTopic
  • h5ad-CLI — command-line tooling for common .h5ad / .zarr operations in bioinformatics workflows
  • peak2vec — Word2Vec-inspired embeddings for chromatin peaks from scATAC-seq data
  • play_around_find_out — notebooks from experiments, prototypes, and “play around and find out” sessions
  • design-patterns — my notes on software design patterns and reusable approaches to writing cleaner code

🛠️ Tech I use often

Python · R · Nextflow · Scanpy · Squidpy · scVI · PyTorch · pandas · NumPy · Docker · Singularity · PostgreSQL

Pinned Loading

  1. spatialMPFC spatialMPFC Public

    Master degree thesis. Analysis of human-specific features of prefrontal cortex spatial organization

    Jupyter Notebook 1

  2. cellgeni/nf-atac cellgeni/nf-atac Public

    Pipeline to process sc-ATAC data with pyCistopic

    Python 4

  3. spitzer-conductivity spitzer-conductivity Public

    Computational solution of spitzer-conductivity problem

    Jupyter Notebook 2 1

  4. Neural-Networks-From-Scratch Neural-Networks-From-Scratch Public

    Implementing simple Neural Networks using numpy

    Python 3

  5. play_around_find_out play_around_find_out Public

    Collection of notebooks with my play around and find out sessions

    Jupyter Notebook

  6. cellgeni/h5ad-cli cellgeni/h5ad-cli Public

    A CLI for operations with AnnData objects in .h5ad and .zarr files

    Python 6