Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS (Nat Biotechnology)

Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistochemistry data. Docs available here: ht…

Predicting tandem mass spectra from molecules

RNA Velocity generalized through dynamical modeling

MUSTANG: reference-free MUlti-sample Spatial Transcriptomics data ANalysis with cross-sample transcriptional similarity Guidance

ExerkineMap is a powerful computational platform designed for spatial biology researchers and pathologists. It integrates single-cell data, multi-omics datasets, and spatial transcriptomics to prov…

A Latex style and template for paper preprints (based on NIPS style)

CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.

This package contains deep learning models and related scripts for RoseTTAFold

Official release of the ProGen models

This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.

WigglyRivers is a Python package that uses wavelet-based methods to create supervised and unsupervised meander identification tools.

Fully local web research and report writing assistant

Common Workflow Language reference implementation

User Friendly Spatial Metabolomic Data Analysis Package

CODEX data processing code

Repository for MolFormer

An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations.

DEEP-GOMS: Deep Learning Predictive Model Gut OncoMicrobiome Signatures project aims to develop a reproducible next-generation biomarker prediction model.

NicheNet: predict active ligand-target links between interacting cells

AUCell: score single cells with gene regulatory networks

R package to infer biological activities from omics data using a collection of methods.

Intel OpenVINO extension for QuPath, a digital pathology platform

SANTO: a coarse-to-fine stitching and alignment method for spatial omics

Mass spectrometry imaging data I/O