Top 40
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Tools & infrastructure
Reproducible software tools for integrating omics and regulatory genomics data analysis
Recent publications add scalable Snakemake, R, and Python tools for multi-omic, chromatin, and variant analysis workflows.
Transcriptomics
Graph neural networks infer spatial domains and niches from expression and histology
Graph-based deep learning is now applied across spatial transcriptomics, histology fusion, and multi-omics feature discovery in recent publications.
Single-cell
Deep generative and contrastive models extend single-cell and multi-omics inference
Recent preprints and publications apply interpretable deep learning to scRNA-seq, scATAC-seq, and spatial data for regulatory and batch-effect analysis.
ML / AI methods
Deep models link histology, imaging and spatial omics to cell and tissue states
Recent preprints apply foundation models, graph networks and contrastive learning across 3D spatial omics, histology and multiplex imaging data.
Single-cell
Computational tools for cell annotation, marker discovery and differential expression
Recent preprints and publications present scalable tools for annotating, visualizing, and validating cell types in single-cell and spatial omics data.