🔍 Explore multimodal omics data easily with `muon`, a powerful Python framework designed for efficient analysis and visualization of diverse biological datasets.

🔬 Explore and analyze multimodal omics data with the muon framework, designed for efficient handling of diverse biological datasets in Python.

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

scverse lineage tracing analysis toolkit

Single-cell analysis in Python. Scales to >100M cells.

Annotated data.

Convert between AnnData and SingleCellExperiment

anndata with trees

muon is a multimodal omics Python framework

🏆 #1 Multi-LLM consensus framework | 550+ stars | 95% accuracy | 10+ LLM providers | Leading cell annotation tool

Single-Cell Atlas Builder: A modular platform for analyzing, integrating, and visualizing single-cell RNA-seq datasets using FastAPI, Scanpy, CellTypist, and optional LLM-powered summaries.

GRaph-based Analysis of Subcellular/Spatial Proteomics

Lightweight, GPU-accelerated single-cell RNA-seq workflow for exploring the colorectal tumor microenvironment (CRC-TME) using Scanpy and scVI.

Sobolev alignment of deep probabilistic models for comparing single cell profiles

A complete single-cell RNA-seq analysis pipeline using Scanpy on 10x Genomics PBMC data, including clustering, UMAP visualization, and marker gene detection.

A collection of Plotly-based functions to visualize Scanpy data mimicking functions from scanpy.pl package.

Cell Analyzer for Flow Experiment

Notes and studies about single-cell RNA-Seq analysis

single cell analysis pipeline and useful tools using scanpy

pseudobulking on an AnnData object