Epigenomics Data Analysis: From Bulk to Single Cell

Contributers

Environment

To be able to contribute to this repository and render files locally, you will need to have Quarto>=1.9.37 installed. This has not been tested on earlier versions of Quarto, so it may still work on older versions.

Once quarto is installed, add the following extensions via the terminal:

quarto add --no-prompt quarto-ext/fontawesome
quarto add --no-prompt royfrancis/quarto-revealjs-header
quarto add --no-prompt royfrancis/quarto-revealjs-pointer
quarto add --no-prompt mcanouil/quarto-collapse-output@1.4.0
quarto add --no-prompt royfrancis/quarto-accordion
quarto add --no-prompt royfrancis/quarto-leaflet
quarto add --no-prompt royfrancis/quarto-team

We will be using R-4.6.1 coupled with Bioconductor release 3.23 for this workshop. Please make sure you are using the right R version when adding new material. If you have multiple R versions installed on your machine, you can use rig to open RStudio with the desired version as follows:

 rig rstudio 4.6 

Setting up a local version of the repo and adding new material

Start by cloning the repository as such:

git clone https://github.com/NBISweden/workshop-epigenomics.git
cd workshop-epigenomics

We will be using renv to keep track of the R packages we are using. The renv.lock file contains all the R packages, under bioc 3.23 which are used in all qmd files. The same lock file is use by github actions to build and deploy the workshop's website.

To add new material, create your own branch and try to use concise and informative names. For example:

# create a new branch locally
git checkout -b addMotifMaterial

# push to remote repo
git push -u origin addMotifMaterial

Alternatively, you can create the new branch on GitHub, pull the updates to your local repo, and switch to that branch to work.

Tip

You can use RStudio to modify your .qmd files and make changes. To do so you will need to create a project. Go to File > New Project > Existing > Directory and add the path to your installed repository called workshop-epigenomics and click 'Create Project'.

Next, we will install the R packages listed in the renv.lock file. You will need to do runt he following commands the first time you are setting up. Make sure that you are using the correct R version and that you are in the root directory of the repo.

# check status
renv:status()

# make sure the library paths are correct (should be pointing to the local renv folder)
.libPaths()

# download the R packages specified in the lock file
renv::restore()

Now you are set up to start making changes and add new material. If there are R packages you are missing, you can either:

1. reach out to Dania, who can add them to the lock file (easiest solution)
2. add them to the lock file yourself as follows:

# check status of packages
# ... this should also report missing packages if they are present in .qmd files 
# ... but not present in the lock file
renv:status()

# install the missing packages
renv::hydrate()

# or: directly install a specific package
# ... always make sure that the .libPaths() are set correctly and that you 
# ... are in the root of the repo
renv::install("myPackage")

# update the lock file
renv::snapshot()

You will notice that the R packages were installed locally under the renv/library folder, which is ignored by git (see renv/.gitignore).

New material can be added by topic as follows:

• slides: presentations/yourTopic
• tutorials: tutorials/yourTopic

PDF slides may be added as presentation. However, if you are comfortable with quarto, we recommend creating quarto presentation to keep the repository at a good size.

Tip

Consider using images in the .webp format to limit the size even more. Below is an example of how you can transfer an image to this format:

cwebp exampleImage.png -o exampleImage.webp

Finally, to visualize how the website may look with your added material, you can run the following from the root:

quarto render

The resulting html files will be outputted under the _site folder. Once you have finalized your changes on your branch, you can create a pull request to the main branch and assign reviewers if you wish.

Students

ToDo: add instruction for students on how they can clone the repo and use the renv lock file to run the tutorials, and how they can access material from previous years.