Computational biologist working across CRISPR screens, genetics, transcriptomics, multi-omics, clinical data and ontologies. Industry background, mostly pharma and biotech. Spare cycles go into open-source tooling: R packages for computational biology and Rust crates that make them fast. Firm believer that good science needs performant open-source software that runs without a fat cloud bill.
Currently playing with burn for deep learning and writing GPU kernels via cubecl.
| Package | Description |
|---|---|
| bixverse | The kitchen sink. Enrichment (GSEA, GSVA, ssGSEA, Gene Ontology with the ontology baked in), matrix factorisations (ICA, NMF, contrastive PCA), gene diffusion, reciprocal best hits, correlation-based methods, and a single cell suite that scales to a million cells on 16 GB without breaking a sweat. |
| bixverse.gpu | SIMD not enough? GPU-accelerated kNN, k-means, correlations, Harmony and sparse PCA for bixverse. Also powers a parametric UMAP for manifoldsR. |
| bixverse.plots | Plotting sub-package. Covers the single cell workflows in bixverse. |
| genewalkR | node2vec interface with a growing collection of graph-heavy computational biology methods: GeneWalk, GeneDrift, random walks and other diffusion approaches. |
| manifoldsR | UMAP, tSNE, PaCMAP, diffusion maps and PHATE (CPU) with swappable ANN back-ends from ann-search-rs. |
Public, MIT licensed, usable on their own if you want to skip R.
| Crate | crates.io | Description |
|---|---|---|
| ann-search-rs |  |
Approximate nearest neighbour search. Highly optimised CPU indices, quantised and binarised variants, plus GPU-accelerated versions. |
| bixverse-rs |  |
Core Rust behind bixverse. GPU-accelerated methods, single cell algorithms, most of the heavy lifting. |
| manifolds-rs |  |
The 2D embedding methods behind manifoldsR. |
| node2vec-rs |  |
node2vec. Optimised CPU implementation plus a burn version from my first trials with the framework. |
| evoc-rs |  |
Rust port of EVoC clustering by Leland McInnes. Exposed via manifoldsR since it uses a UMAP-like backbone. |