SkinOmicsExplorer

SkinOmicsExplorer is an interactive R Shiny portal for exploring and querying the multi-omics datasets generated in:

Yuqing et al.
A Spatially Coordinated Keratinocyte–Fibroblast Circuit Recruits MMP9⁺ Myeloid Cells to Drive IFN-I-Driven Inflammation in Photosensitive Autoimmunity
Yuqing Wang, Khashayar Afshari, Nazgol-Sadat Haddadi, Carolina Salomão Lopes, Chee-Huat Linus Eng, Nuria Martinez, Leah Whiteman, Ksenia S Anufrieva, Kevin Wei, Kirsten Frieda, Stefania Gallucci, Misha Rosenbach, Ruth Ann Vleugels, John E Harris, Mehdi Rashighi, Manuel Garber bioRxiv 2025.08.19.670635; doi: https://doi.org/10.1101/2025.08.19.670635

The portal integrates:

• single-cell RNA sequencing
• spatial transcriptomics (seqFISH)
• bulk RNA-seq
• targeted proteomics (OLINK & NULISA)

to enable interactive visualization of gene and protein expression across diseases, cell types, spatial contexts, and experimental perturbations.

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Key features

• Interactive scRNA-seq UMAP embeddings and gene expression plots
• Spatial visualization of seqFISH data across disease and UV perturbations
• Targeted proteomics visualization for in vivo and in vitro experiments
• Bulk RNA-seq perturbation analysis
• Publication-ready plot export (PNG/PDF)
• Multi-gene heatmap generation

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Supporting repositories

SkinOmicsExplorer builds on custom visualization and analysis frameworks developed in:

• AddOns — reusable Shiny modules and visualization utilities
  https://github.com/mgarber/AddOns

• scSpatial — spatial transcriptomics processing and visualization tools
  https://github.com/Yuqing66/scSpatial

These repositories provide core functionality for interactive plotting, spatial rendering, and multi-omics integration.

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Running

Docker images are available for easy running of the portal without installing dependencies

docker pull yuqing987/r-skinomicsexplorer-arm

docker run -p 8888:8888 \
  -v "./shinyApp_content":/home/app_data/ \
  -it yuqing987/r-skinomicsexplorer-arm:latest

Citation

Yuqing et al. A Spatially Coordinated Keratinocyte–Fibroblast Circuit Recruits MMP9+ Myeloid Cells to Drive IFN-I-Driven Inflammation in Photosensitive Autoimmunity. Nature Immunology (accepted)