Repository Index

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

Fusing Histology and Genomics via Deep Learning - IEEE TMI

• pathomic
• fusion
• multimodal
• pathology

Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome

• cancer-genomics
• cnv-detection
• single-cell
• phylogeny

Probabilistic cell segmentation for in situ spatial transcriptomics

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

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

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution