TreeTag is a fast, interpretable, and recursive marker-based cell annotation method for single-cell RNA-seq data.

CUDA Python: Performance meets Productivity

single-cell latent diffusion model

Distributed single-cell data analysis.

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

Python 3.8+ toolbox for submitting jobs to Slurm

Conveniently process a dictionary of anndatas

Flow-based model for learning non-gradient field dynamics

Fast array utilities

Labs for MIT 6.S184/6.S975, IAP 2025

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

Benchmarking pipeline for single-cell perturbation prediction tools

scverse context for agentic coding

Multi-Omics Factor Analysis

Run embedding comparisons for single-cell data

A computational toolkit in R for the integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.

Generation of disentangled microenvironment-induced and intrinsic gene expression vectors from spatial transcriptomics data

Benchmark of GRNs using the GRETA pipeline

LLM-powered personalized daily lists of scientific papers

Access & manage biological ontologies.

Toolbox for single-cell data analysis on sample level

Spatially resolved transcriptomic analysis

Predicting the profiles of one modality (e.g. protein abundance) from another (e.g. mRNA expression).

A novel method for single-cell diagonal integration: scConfluence