geneformer

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

Code, results and paper for "The geometry of single-cell foundation models: what they inherit, what they add, and what shapes it"

Reproducible Geneformer analysis environments with uv

A confound-aware toolkit for evaluating foundation-model in-silico perturbation predictions.

Fine-tuned Geneformer vs. a PCA baseline for scRNA-seq cell-type annotation, as a reproducible containerized HPC pipeline.

scFM-Perturb-Bench: scalable scRNA-seq perturbation & gene-synergy benchmark with Geneformer · GSEA · Scanpy. Audit multi-gene interactions & drug-target potential — GPU/Docker ready foundation-model pipeline.

Companion code for the PLOS ONE paper 'What topological and geometric structure do biological foundation models learn? Evidence from 141 hypotheses'.

Cross-cohort benchmarking of frozen Geneformer and expression pseudobulk for donor-level SLE classification