Rapid GPU accelerated segmentation and counting of adipocytes from histology slides.

Spatial transcriptomics foundation model based on Graph Transformer and JEPA

Makes your AI agent think like the laziest senior dev in the room. The best code is the code you never wrote.

Gephi - The Open Graph Viz Platform

An agent that takes a dead research repo and turns it into a callable pipeline component.

registration package

INSPIRE: interpretable, flexible and spatially-aware integration of multiple spatial transcriptomics datasets from diverse sources

A Nextflow pipline for running single cell post processing

Self-hosted AI workspace.

A public MuSpAn page for community discussions and issue reporting.

Python Reimplementation of the soupx scRNA ambient removal package

Robust and scalable single-cell signature scoring

Tissue perturbation modeling with spatially resolved single-cell transcriptomics

Fast genomics quality control tools for sequencing data, written in Rust.

Piecewise alignment for layers of mosaics

An AnnData-based framework for integrated proteomics analysis

R-based Xenium Spatial Analysis Toolkit to assess gene expression gradients

Vim-fork focused on extensibility and usability

A Cytoscape Jupyter widget

NDEx application code examples in Jupyter notebooks

Metric learning-based graph-partitioned trajectory inference from single-cell data

Official code repo for the O'Reilly Book - "Hands-On Large Language Models"

MCP server for spatial transcriptomics analysis through natural language interfaces.

A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

Retrieve author and publication information from Google Scholar in a friendly, Pythonic way without having to worry about CAPTCHAs!

π RuView turns commodity WiFi signals into real-time spatial intelligence, vital sign monitoring, and presence detection — all without a single pixel of video.

GitNexus: The Zero-Server Code Intelligence Engine - GitNexus is a client-side knowledge graph creator that runs entirely in your browser. Drop in a git repository (Github, Gitlab, Azure, Local) or…

A minimal PyTorch re-implementation of AlphaFold2's model & training

Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.