scvi-tools

Accelerated, Python-only, single-cell integration benchmarking metrics

Notebooks used in scvi-tools tutorials

Template repository for creating novel models with scvi-tools

A PKHeX compatible dumper and injector for Pokémon Scarlet and Violet.

Brain-Referenced In vivo-to-in vitro Developmental Guidance and Evaluation.

scVIVA-Tools: A unified toolkit for spatial transcriptomics analysis

Deep Learning Based Models for Preimplantation Mouse and Human Development

Sobolev alignment of deep probabilistic models for comparing single cell profiles

Variational Inference for Cell Type Evolution

scANVI Explainer

MCP (Model Context Protocol) server for deep probabilistic analysis of single-cell omics data using scvi-tools

Lightweight helper to install scvi-tools in Google Colab

scRNA Analysis tutorials

Code for the MiSTR microfluidic stem cell atlas study of early human neural patterning.

Single-cell RNA-seq analysis of mouse gastrulation using data from Argelaguet and Pijuan-Sala. The project includes preprocessing, SCVI-based dataset integration, differential gene expression analysis, and a no-code interface powered by Chatmol for natural language interaction with the pipeline.

Reproducible single-cell framework for immune aging using scVI, donor-aware analyses, molecular signatures, and age prediction.

Reproducibility project for Melms et al. (Nature 2021) COVID-19 single-nucleus RNA-seq lung atlas

End-to-end single-cell RNA-seq pipeline with scVI, Scanpy, and CellTypist for QC, clustering, annotation, and differential expression.