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

Annotated data.

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

muon is a multimodal omics Python framework

Convert between AnnData and SingleCellExperiment

Learning cell communication from spatial graphs of cells

Multi-agent driven cell type annotation for single-cell RNA-Seq data stored in Anndata format

pseudobulking on an AnnData object

Notes and studies about single-cell RNA-Seq analysis

An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)

anndata with trees

Sobolev alignment of deep probabilistic models for comparing single cell profiles

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Cell Analyzer for Flow Experiment

GRaph-based Analysis of Subcellular/Spatial Proteomics

Multimodal datasets, in MuData format

scverse lineage tracing analysis toolkit

A bioinformatics web app for single cell RNA seq analysis.

Intuitive Nonparametric Gene Network Search Algorithm