Welcome to SeptiSearch, an interactive Shiny app providing access to manually-curated molecular sepsis data from current publications. Visit us at septisearch.ca! And be sure to check out our publication in Frontiers in Immunology: doi: 10.3389/fimmu.2023.1135859
The SeptiSearch app is designed to allow easy access to curated sepsis gene sets. Multiple tabs allow the exploration and use of the data in a number of ways:
- Explore the Database makes it easy to search all curated gene sets by keyword or molecule, filter with select criteria, and view all the molecules in a gene set
- Visualize the Database plots the most common molecules, and provides filters to see which occur most frequently based on a number of attributes
- Perform Pathway Enrichment allows users to upload their own list of genes, or use one of the curated sepsis gene sets, to test for enriched pathways/terms using ReactomePA and EnirchR
- Test for Enriched Sepsis Gene Sets can be used to test your own expression data (e.g. counts from RNA-Seq) for dysregulation of the curated sepsis gene sets
For more details on how to use SeptiSearch, please see our tutorial hosted via Github pages: https://hancockinformatics.github.io/SeptiSearch/
SeptiSearch uses the following R packages:
A big thank you to all of the SeptiSearch beta testers from the Hancock Lab: Morgan Alford, Andy An, Melanie Dostert, Evan Haney, and Felix Santana.
Travis Blimkie is the main developer of the Shiny app. Jasmine Tam performed all of the data gathering and curation, while Arjun Baghela served as the supervisor for the project.
This project uses the GNU General Public License v3.0, available here.
