Updated README.md file

README.md

@@ -1,52 +1,33 @@
-# BuildABiocWorkshop
+## Overview
 
-This package is a template for building a Bioconductor workshop. The package
-includes Github actions to:
+clustSIGNAL is an R package that performs spatially-resolved clustering on spatial transcriptomics data. It uses an entropy-guided approach to measure the "domainness" of cell neighbourhoods - homogeneous neighbourhoods have low entropy and heterogeneous neighbourhoods have high entropy. The entropy values are used to generate cell neighbourhood-specific weights to perform an adaptive smoothing of gene expression - smoothing is performed over more cells in homogeneous neighbourhoods, but heterogeneous neighbourhoods are smoothed over a much smaller region. This approach aims to overcome data sparsity in spatial transcriptomics gene expression, while incorporating spatial context in the form of cell arrangement information of each cell's neighbourhood.
 
-1. Set up bioconductor/bioconductor_docker:devel on Github resources
-2. Install package dependencies for your package (based on the `DESCRIPTION` file)
-3. Run `rcmdcheck::rcmdcheck`
-4. Build a pkgdown website and push it to github pages
-5. Build a docker image with the installed package and dependencies and deploy to [the Github Container Repository](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry#pulling-container-images) at the name `ghcr.io/gihub_user/repo_name`, all lowercase. 
 
-## Responsibilities
 
-Package authors are primarily responsible for:
+## Pre-requisites to run the workshop
 
-1. Creating a landing site of their choosing for their workshops (a website). This website should be listed in the `DESCRIPTION` file as the `URL`.
-2. Creating a docker image that will contain workshop materials and the installed packages necessary to run those materials. The name of the resulting docker image, including "tag" if desired, should be listed in a non-standard tag, `DockerImage:` in the `DESCRIPTION` file. 
+The attendees are expected to have:
 
-Both of those tasks can be accomplished using the Github actions included in this template package. The vignette accompanying this package describes how to accomplish both of these tasks.
+1. Experience with R programming, and
+2. Familiarity with SingleCellExperiment and/or SpatialExperiment objects.
 
-## Details
 
-For detailed instructions, see the `How to build a workshop` article/vignette.
 
-## Results of successful deployment
+## Content and objective
+Below is a list of tasks we will go through during the workshop, and what the attendees can expect to learn from them.
 
-- A working docker image that contains the installed package and dependencies.
-- An up-to-date `pkgdown` website at https://YOURUSERNAME.github.io/YOURREPOSITORYNAME/
-- Docker image will be tagged with `latest`, `sha-XXXXXX` where `XXXXXX` is the hash of the current `master` commit, and `master`. 
+| Task                                       | Objective   |
+|--------------------------------------------|-------------|
+| Concept behind clustSIGNAL                 | Discription of how clustSIGNAL works as a spatial clustering method. How does clustSIGNAL embed spatial information into the data and how that affects clustering.
+| Method parameters                          | Learn about the different clustering parameters available in clustSIGNAL, and understand how they can affect the clustering output. 
+| How to run clustSIGNAL                     | Perform clustering on spatial transcriptomics data with clustSIGNAL. Also, learn what sort of outputs can be obtained from running the method.
+| Assessing biological relevance of clusters | Investigate the biological relevance of the clusters obtained from running clustSIGNAL.
+| Exploring clustSIGNAL outputs              | Learn about how some of the data generated by clustSIGNAL can be useful for other analyses.
 
-## To use the resulting image:
 
-```sh
-docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME
-```
-Once running, navigate to http://localhost:8787/ and then login with `rstudio`:`yourchosenpassword`. 
 
-To try with **this** repository docker image:
+## Notes
 
-```sh
-docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/bioconductor/buildabiocworkshop
-```
+The clustSIGNAL R package is available to download and install from [github/SydneyBioX/clustSIGNAL](https://github.com/SydneyBioX/clustSIGNAL).
 
-*NOTE*: Running docker that uses the password in plain text like above exposes the password to others 
-in a multi-user system (like a shared workstation or compute node). In practice, consider using an environment 
-variable instead of plain text to pass along passwords and other secrets in docker command lines. 
-
-
-## Whatcha get
-
-- https://bioconductor.github.io/BuildABiocWorkshop
-- A Docker image that you can run locally, in the cloud, or (usually) even as a singularity container on HPC systems. 
+The attendees can bring their own data, and run the method locally.