Update README.md

Author: travis-m-blimkie

README.md

@@ -1,103 +1,30 @@
-# just-the-docs-template
-
-This is a *bare-minimum* template to create a [Jekyll] site that:
-
-- uses the [Just the Docs] theme;
-- can be built and published on [GitHub Pages];
-- can be built and previewed locally, and published on other platforms.
-
-More specifically, the created site:
-
-- uses a gem-based approach, i.e. uses a `Gemfile` and loads the `just-the-docs` gem;
-- uses the [GitHub Pages / Actions workflow] to build and publish the site on GitHub Pages.
-
-To get started with creating a site, just click "[use this template]"!
-
-After completing the creation of your new site on GitHub, update it as needed:
-
-## Replace the content of the template pages
-
-Update the following files to your own content:
-
-- `index.md` (your new home page)
-- `README.md` (information for those who access your site repo on GitHub)
-
-## Changing the version of the theme and/or Jekyll
-
-Simply edit the relevant line(s) in the `Gemfile`.
-
-## Adding a plugin
-
-The Just the Docs theme automatically includes the [`jekyll-seo-tag`] plugin.
-
-To add an extra plugin, you need to add it in the `Gemfile` *and* in `_config.yml`. For example, to add [`jekyll-default-layout`]:
-
-- Add the following to your site's `Gemfile`:
-
-  ```ruby
-  gem "jekyll-default-layout"
-  ```
-
-- And add the following to your site's `_config.yml`:
-
-  ```yaml
-  plugins:
-    - jekyll-default-layout
-  ```
-  
-Note: If you are using a Jekyll version less than 3.5.0, use the `gems` key instead of `plugins`.
-
-## Publishing your site on GitHub Pages
-
-1.  If your created site is `YOUR-USERNAME/YOUR-SITE-NAME`, update `_config.yml` to:
-
-    ```yaml
-    title: YOUR TITLE
-    description: YOUR DESCRIPTION
-    theme: just-the-docs
-
-    url: https://YOUR-USERNAME.github.io/YOUR-SITE-NAME
-
-    aux_links: # remove if you don't want this link to appear on your pages
-      Template Repository: https://github.com/YOUR-USERNAME/YOUR-SITE-NAME
-    ```
-
-2.  Push your updated `_config.yml` to your site on GitHub.
-
-3.  In your newly created repo on GitHub:
-    - go to the `Settings` tab -> `Pages` -> `Build and deployment`, then select `Source`: `GitHub Actions`.
-    - if there were any failed Actions, go to the `Actions` tab and click on `Re-run jobs`.
-
-## Building and previewing your site locally
-
-Assuming [Jekyll] and [Bundler] are installed on your computer:
-
-1.  Change your working directory to the root directory of your site.
-
-2.  Run `bundle install`.
-
-3.  Run `bundle exec jekyll serve` to build your site and preview it at `localhost:4000`.
-
-    The built site is stored in the directory `_site`.
-
-## Publishing your built site on a different platform
-
-Just upload all the files in the directory `_site`.
-
-## Customization
-
-You're free to customize sites that you create with this template, however you like!
-
-[Browse our documentation][Just the Docs] to learn more about how to use this theme.
-
-----
-
-[^1]: [It can take up to 10 minutes for changes to your site to publish after you push the changes to GitHub](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/creating-a-github-pages-site-with-jekyll#creating-your-site).
-
-[Jekyll]: https://jekyllrb.com
-[Just the Docs]: https://just-the-docs.github.io/just-the-docs/
-[GitHub Pages]: https://docs.github.com/en/pages
-[Bundler]: https://bundler.io
-[use this template]: https://github.com/just-the-docs/just-the-docs-template/generate
-[`jekyll-default-layout`]: https://github.com/benbalter/jekyll-default-layout
-[`jekyll-seo-tag`]: https://jekyll.github.io/jekyll-seo-tag
+# SeptiSearchTutorial
+
+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](https://septisearch.ca).
+
+The SeptiSearch tutorial docs were created using JustTheDocs; more information 
+is available [here](https://just-the-docs.github.io/just-the-docs/).
+
+## SeptiSearch overview
+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
+
+## License
+This project uses the MIT license, available
+[here](https://github.com/hancockinformatics/SeptiSearchTutorial/blob/main/LICENSE).