Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

De novo reconstruction of cell interaction landscapes from single-cell spatial transcriptome data

Multi-level Graph Autoencoder (GAE) to clarify cell cell interactions and gene regulatory network inference from spatially resolved transcriptomics

Implementation of multiplex Leiden for analysis of spatial omics data

Extremely fast non-cryptographic hash algorithm

Apache Arrow is the universal columnar format and multi-language toolbox for fast data interchange and in-memory analytics

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Documentation that simply works

Simple tool for clustering spatial points with categorical labels.

Uniform Manifold Approximation and Projection

Public repository for Agent Skills

Fast, sensitive and accurate integration of single-cell data with Harmony

KeePassXC is a cross-platform community-driven port of the Windows application “KeePass Password Safe”.

R SDK for interacting with Microsoft 365 APIs

Parallel computing with task scheduling

rapids_singlecell: GPU-accelerated framework for scRNA analysis

https://sparrow-pipeline.readthedocs.io/en/latest/

A dependency-free large (+2500) collection of colormaps and palettes for Python 🎨

🔬 MCP server for AI-powered napari control. Connect Claude, ChatGPT, Cursor, and other LLMs to napari for interactive image analysis. Perfect for automating microscopy workflows and building intell…

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation)

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