Optimized pipelines for Spatial Transcriptomics (ST) data analysis using Seurat & Giotto, designed for reproducible benchmarking and biological insight.

Identifying cell-type-specific spatially variable genes

Decoding the Archetypes and Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy

Spatial-sequencing: The final frontier. These are the voyages of the 10x Visium pipeline, space-seek.

single-cell RNA-seq, spatial transcriptomics, and spatial proteomics analysis skills

Spatial Transcriptome

A python toolkit for spatial domains and spatially variable genes discovery for high-resolution spatially resolved transcriptomics data.

A R package for deconvolving low‐resolution Visium HD spatial data back to high‐resolution spots via barcode‐ and coordinate‐based methods, with built‐in visualization.

🔬 Benchmark Spatial Transcriptomics data analysis with optimized pipelines using Seurat and Giotto for reproducible results and biological insights.