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Croissant is a high-level format for machine learning datasets that brings together four rich layers.

Jupyter Notebook 669 73 Updated Jul 11, 2025

An open-source AI agent that brings the power of Gemini directly into your terminal.

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A CodecPipeline for zarr-python backed by zarrs (Rust)

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State is a machine learning model that predicts cellular perturbation response across diverse contexts

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ZenML 🙏: The bridge between ML and Ops. https://zenml.io.

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I wrote a python native Kubernetes workflow orchestrator

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🤗 The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient data manipulation tools

Python 20,366 2,866 Updated Jul 9, 2025

Business intelligence as code: build fast, interactive data visualizations in SQL and markdown

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Lightweight lockfile for conda environments

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This is the development home of the workflow management system Snakemake. For general information, see

Python 2,521 603 Updated Jul 10, 2025

Conditionally run actions based on files modified by PR, feature branch or pushed commits

TypeScript 2,583 305 Updated Aug 20, 2024

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

Python 178 52 Updated Jun 19, 2025

Genome modeling and design across all domains of life

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Arc Virtual Cell Atlas

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Report GitHub Actions build status on Slack

JavaScript 4 2 Updated Mar 16, 2024

Distributed single-cell data analysis.

Jupyter Notebook 31 3 Updated Jul 10, 2025

A light-weight, flexible, and expressive statistical data testing library

Python 3,912 350 Updated Jul 8, 2025

A fast yet powerful Python Markdown parser with renderers and plugins.

Python 2,829 258 Updated May 21, 2025

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Python 659 76 Updated Jul 8, 2025

R Interface to Python

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Parse and execute ipynb files in Sphinx

Jupyter Notebook 226 90 Updated Jul 13, 2025

Manage projects & references.

Python 2 Updated Jan 18, 2025

An example analysis to demonstrate laminr

1 Updated Nov 21, 2024

Sharchaea: the top predator of the microbial world

Perl 1 Updated Apr 23, 2015

OMOP Common Data Model.

Python 2 Updated Feb 16, 2025

A reference manager.

Python 2 Updated Jan 7, 2025

A schema for clinical metadata.

Python 1 Updated Jun 1, 2025

Genomic interval operations on Pandas DataFrames

Python 184 35 Updated Jul 7, 2025
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