Attach and AnnData file in duckdb and query it with SQL. Perform SQL over groups of AnnData files

Hands-on AlphaFold implementation for educational purposes.

R Data Deserialization in python

Paper2Agent is a multi-agent AI system that automatically transforms research papers into interactive AI agents with minimal human input.

Democratizing AI scientists with ToolUniverse

Biomni: a general-purpose biomedical AI agent

An Agentic AI Framework for Ingestion and Standardization of Single-Cell RNA-seq Data Analysis

The Open Source kanban, built with Meteor. GitHub issues/PRs are only for FLOSS Developers, not for support, support is at https://wekan.fi/commercial-support/ . New English strings for new feature…

Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data

DenoIST: Denoising Image-based Spatial Transcriptomics data

The AnnSQL package enables SQL based queries on AnnData objects.

Learn python3 in one picture.

Single-cell epigenomics analysis tools

Python implementation of Milo for differential abundance testing on KNN graph

Python interface to Graphviz graph drawing package

🔬 Path to a free self-taught education in Bioinformatics!

Python package to interactively annotate histological images within a jupyter notebook

An introduction to OME-Zarr for big bioimaging data

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

Interactive network visualization in Python and Dash, powered by Cytoscape.js

Extracellular vesicles-mediated intercellular communication networks

📚 Parameterize, execute, and analyze notebooks

List of Spatial Transcriptomics related Tools organized per category

Spatial bivariate association tests for multi-omics data with disjoint coordinate sets

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…

Accessible and interoperable whole slide image analysis

Easily read and write ome-tiff images in python