Developing FAIR open-source interactive web browsers for individual labs to explore single-cell data: Shiny-PIGGI as an example from the AgBioData Single Cell Working Group.

Authors: KAPOOR, MUSKAN - Iowa State University; Wiarda, Jayne; Loving, Crystal; KUMARI, SUNITA - Cold Spring Harbor Laboratory; Ware, Doreen; TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/9/2026
Publication Date: 1/9/2026
Citation: Kapoor, M., Wiarda, J.E., Loving, C.L., Kumari, S., Ware, D., Tuggle, C.K. 2026. Developing FAIR open-source interactive web browsers for individual labs to explore single-cell data: Shiny-PIGGI as an example from the AgBioData Single Cell Working Group. . Plant and Animal Genome Conference. Plant and Animal Genome Conference.

Interpretive Summary:

Technical Abstract: The AgBioData Single Cell Biocuration working group is developing a comprehensive framework for implementing FAIR data principles for agricultural single-cell (SC) genomics. Through this working group, we are working on assessing existing SC resources and identifying the critical gaps in current infrastructure, particularly the need for accessible, lab-level tools that enable interactive data exploration without requiring extensive bioinformatics expertise. While SC transcriptomics has revolutionized our understanding of cellular heterogeneity, particularly in agriculturally important species, most existing resources require specialized computational skills, limiting broader community engagement with these valuable datasets. The porcine immune system serves as an ideal model for addressing this challenge. Pigs are not only crucial as a food source but also serve as valuable biomedical models due to their physiological similarity to humans. Recent SC transcriptomics studies of porcine lymphoid organs have generated rich datasets characterizing immune cell populations across tissues, yet these data remain underutilized due to accessibility barriers. To address this gap, we have developed Shiny-PIGGI (Porcine Immune Genomics Gateway Interface), an open-source, domain-agnostic web application framework that empowers individual laboratories to interactively explore multi-tissue SC RNA-seq data. Shiny-PIGGI is provided as a containerized resource that does not require modification of user computational environment or programming expertise. This design aligns with FAIR data principles by enhancing data accessibility, interoperability and reusability. We deployed Shiny-PIGGI as a proof-of-concept using porcine immune data sets including bone marrow, spleen, thymus, and lymph nodes. This interactive platform enables users to perform gene expression queries, compute differential gene expression across tissues and cell types, interactive visualization of cell type distributions using UMAP/t-SNE projections, and cross tissue reference mapping comparisons to identify conserved and tissue specific immune populations. Shiny-PIGGI’s modular architecture enables rapid adoption to SC datasets from any agricultural species and tissue type. Moving forward, we are actively collaborating with AgBioData community to integrate additional agricultural SC datasets including cattle, poultry and major crop species, establishing a growing ecosystem of interactive atlases. We are also developing standardized data submission pipelines to enable researchers to contribute their own datasets, fostering community-driven expansion. Training workshops and comprehensive tutorials will be provided to support widespread adoption and empower laboratories with limited computational resources. Shiny-PIGGI is publicly accessible at http://shinypiggi.ansci.iastate.edu, with comprehensive documentation, source code and installation instructions available at https://github.com/kapoormuskan/Pig_Immune_Tissue_ShinyApp. By lowering technical barriers to SC data exploration, Shiny-PIGGI advances the AgBioData mission of making agricultural genomics data truly FAIR and broadly accessible.