Zhengyu Ouyang

Spatial transcriptomics reveals heterogeneous cell-cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions

The paper uses spatial transcriptomics to analyze cell-cell interactions in a cuprizone model, finding region-specific changes and partial translatability to multiple sclerosis lesions.

SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

SpaceSequest provides a unified pipeline for analyzing spatial transcriptomics data from multiple platforms, enabling standardized processing, analysis, and visualization.

CompBioAgent: an LLM-powered agent for single-cell RNA-seq data exploration

CompBioAgent provides a user-friendly tool powered by LLMs to explore scRNA-seq data through natural language queries and visualizations.

ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU.

ScaleSC provides a GPU-accelerated single-cell RNA-seq analysis pipeline with 20x speedup and scalability for large datasets.

Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases

The paper integrates brain RNA-seq and genotype data to identify eQTLs and their downstream effects on brain-related diseases.

CellDepot: A unified repository for scRNA-seq data and visual exploration

CellDepot provides a web platform for uploading, querying, and comparing scRNA-seq datasets with visualization tools to support data sharing and analysis.

CellMap: Characterizing the types and composition of iPSC-derived cells from RNA-seq data

CellMap infers cell type profiles in bulk RNA-seq data from iPSC-derived cell lines using reference single-cell datasets.

Cellxgene VIP unleashes full power of interactive visualization and integrative analysis of scRNA-seq, spatial transcriptomics, and multiome data

Cellxgene VIP enhances single cell data analysis by providing interactive visualization, advanced analytical tools, and multi-modal data integration for scRNA-seq, spatial transcriptomics, and multiome datasets.

MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function

MAGGIE identifies DNA sequence motifs mediating TF binding and function by linking genetic variation to epigenomic changes, improving sensitivity and specificity over existing methods.