Starred repositories
STHD: probabilistic cell typing of Single spots in whole Transcriptome spatial data with High Definition
Extended Path2Space code: analysis and downstream methods.
Companion code for Shulman et al., Cell 2026: AI-predicted spatial transcriptomics unlocks breast cancer biomarkers from pathology.
Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing
A dynamic inference method in latent space for omics data.
Collection of custom code central to major analyses in GBMspace
Notebooks and scripts used to analyse GBM multi-ome atlas
scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (eGRNs) from single-cell multiome data (RNA + ATAC).
Configure Vitessce using existing Scverse plotting APIs
Custom scripts for spatial omics alignment, metabolite resampling, registration QC and robustness analyses.
WordCraft: an open-source, clean-room word processor in pure Rust
Repository for Immune Atlas Research Consortium at MMRF for storing research project code
Analysis for our 2018 Immunity paper (cell atlas of mouse thymus development).
source code of scDeepID used in TenK10K manuscripts
The computational and statistical analyses of TenK10K phase 1 multiome data