Welcome to SeptiSearchTutorial, the GitHub repository holding the documentation for SeptiSearch, an interactive Shiny app providing access to manually-curated molecular sepsis data from current publications. Visit the main site at septisearch.ca.
The SeptiSearch tutorial docs were created using JustTheDocs; more information is available here.
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
This project uses the MIT license, available here.