By: Joe Hou
This Shiny application provides an interactive interface for exploring 10X scRNAseq data derived from HSV+ skin biopsy samples. [Access the Application Here](http://34.220.16.45:7777/). As the manuscript is currently under review for publication, the raw and processed data remain undisclosed.
- About the cohort:
This study involved healthy adults with confirmed herpes simplex virus type 2 (HSV-2) seropositivity, verified via Western blot analysis. All participants tested negative for HIV. In this longitudinal HSV study, we enrolled 17 participants and collected genital skin biopsies at three distinct time points to capture HSV shedding and healing phases.
- About the time points:
Samples were collected at three key stages: the first, labeled "Prior," was collected before any visible lesions appeared. When lesions became visible, samples were labeled as "Lesion." Finally, samples taken 8 weeks after lesion appearance are referred to as "Post."
- About the dataset:
This release includes datasets with refined mapping for T cells and Myeloid cells. Users can freely select from the available datasets for exploration. We recommend using the "CellType_Level3" annotation for visualization, as it provides the most detailed and granular clustering. While "CellType_Level1" offers a broader categorization, "CellType_Level3" represents the final, detailed clustering, with cell types identified at a higher level of specificity. Full definitions of each cell cluster and cell type will be provided in the manuscript upon publication.
(1) Cell Cluster Composition:
- Goal: Analyze the composition of cell clusters across time points and individuals, with some clusters showing specificity to time points and variability across participants.
(2) Gene Expression Patterns:
- Goal: Investigate gene expression patterns across different cell clusters, including gene distribution and expression variability across time points.
Here are some visual showcases of the application features:
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Nov-1-2024: release ver 1.0