Data intensive science for everyone.

Accepted JOSS papers

Docker container recipes for CCBR

usegalaxy.* common tools

example templates for galaxy

A Grammar of Graphics for Python

The official Python SDK for the Foundry API

20250517_spac

A collection of Galaxy-related training material

Foundation Model for Multiplex Spatial Proteomic Images

Lightweight coding agent that runs in your terminal

WDL Analysis Research Pipelines

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Workflow Package for Analysis of Single Cell Data

HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

Spot pseudo-Imager on top of histology

Methods for visualization and analysis of spatially-resolved gene expression

Shiny for Python

The Shiny Interactive Realtime Dashboard for SPAC

中文翻译的 Hands-On-Large-Language-Models (hands-on-llms)，动手学习大模型

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

Demo workflow with SPAC package

Hamilton helps data scientists and engineers define testable, modular, self-documenting dataflows, that encode lineage/tracing and metadata. Runs and scales everywhere python does.

High quality resources & applications for LLMs, multi-modal models and VectorDBs

GraphRAG database - hybrid graph / vector db