Aljes Binkevich Claptar

🌥️

13 followers · 31 following

@cellgeni
Cambridge, UK
11:06 (UTC +01:00)
https://orcid.org/0009-0003-1467-1606
in/claptar

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Overview Repositories 28 Projects Packages Stars 107

Overview
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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

spatialMPFC spatialMPFC Public

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

Jupyter Notebook 1
cellgeni/nf-atac cellgeni/nf-atac Public

Pipeline to process sc-ATAC data with pyCistopic

Python 4
spitzer-conductivity spitzer-conductivity Public

Computational solution of spitzer-conductivity problem

Jupyter Notebook 2 1
Neural-Networks-From-Scratch Neural-Networks-From-Scratch Public

Implementing simple Neural Networks using numpy

Python 3
play_around_find_out play_around_find_out Public

Collection of notebooks with my play around and find out sessions

Jupyter Notebook
cellgeni/h5ad-cli cellgeni/h5ad-cli Public

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

Python 6

Claptar (Aljes Binkevich) · GitHub