This tool allows you to spatially plot expressed genes and transcriptional signatures on various datasets generated using spatial transcriptomics technology (Visium)

Publication: "Assessment of Spatial Genomics for Oncology Discovery" Cell Reports Methods (2022)

10X Visium: This technology allows for the capture of whole transcriptome information from tissue sections while preserving specific tissue context.

Tissues: These datasets come from the following models:

1. Healthy rat colon
2. Syngeneic mouse tumor models (B16, MC38)
3. Human PDAC (Donors A, B, and C)

Signatures: These gene signatures were gathered from tissue- and indication- specific publications and curated manually. (See Supplementary Table 1 for more information about the signatures)

Citation: Lyubetskaya A, Rabe B, Fisher A, Lewin A, Neuhaus I, Brett C, Brett T, Pereira E, Golhar G, Kebede S, Font-Tello A, Mosure L, Van Wittenberghe N, Mavrakis K, MacIsaac K, Chen B, Drokhlyansky E (2022). “Assessment of Spatial Genomics for Oncology Discovery”. Cell Reports Methods. doi: TBA

Raw Data: Available under GEO GSE211895

Feedback: We welcome any feedback including signature and data issues -- please contact Anna Lyubetskaya and Eugene Drokhlyansky.

This Shiny application utilizes CanvasXpress to provide interactive performant visualizations. For more information on this technology visit https://canvasxpress.org/

Codebase: https://github.com/anvaly/SpatialPortal

License: GNU General Public License v3.0 - see LICENSE.md