Repository Index

Code for the ProteinMPNN paper

Deep probabilistic analysis of single-cell and spatial omics data

• scrna-seq
• variational-bayes
• variational-autoencoder
• cite-seq

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.

• analysis
• claude
• claudecode
• dna

Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal