GPU accelerated post-processing for 2D or 3D iterative barcoded FISH data.

OS-ATLAS: A Foundation Action Model For Generalist GUI Agents

Read and write Neuroglancer datasets programmatically.

BANKSY: spatial clustering

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

Visual Studio Code

Get up and running with Llama 3.3, DeepSeek-R1, Phi-4, Gemma 3, and other large language models.

Module for embedding igv.js in an IPython notebook

peakHiC method to identify 3D chromatin interactions (loops) from HiC data

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Python project containing Ice remoting code for OMERO

Static plotting for spatialdata

Multi-Omics Factor Analysis

🧡 Follow everything in one place

A nextflow pipeline which integrates multiple omic data streams and performs coordinated analysis

An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

Probabilistic cell segmentation for in situ spatial transcriptomics

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

An AI Agent for Fully Automated Multi-omic Analyses

Agent Zero AI framework

Run PyTorch LLMs locally on servers, desktop and mobile

Utilities intended for use with Llama models.

🎓 无需编写任何代码即可轻松创建漂亮的学术网站 Easily create a beautiful academic résumé or educational website using Hugo and GitHub. No code.

One downloader for many scientific data and code repositories! DOI 👐 Data

Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.