Projects, Rstudio, and going forward

Why are we using github to start with?

github provide a useful way for us to collaborate and to help each other with analyses. Of particular use is that it provides a nice way for us to share code so that we don't have to reinvent the wheel each time we want to do something. We're hoping to overtime build up a 'database' of common functions performed in our analyses

The approach we're going to take is to store code (preferrably Rmarkdown) here and have the datasets stored on the XSan so that we maintain the security of datasets but have reproducibility and transparency of analyses increased.

Compartmentalisation

Now that you have completed the initial tutorial we're going to revisit a few things and make them applicable to future usage.

You will notice that in following the tutorial that you created a new project in RStudio and for that project we have a single repository associated with it.

By having a single repository with a single project allows us to compartmentalise analyses. So if for example you were working on the resequencing project you can go to our repository here on github and follow the same steps you did to initialise a project but this time using the repository details from the resequencing page.

You can then either create a new R script/ R markdown or continue a already established file (be mindful that you might be changing someone else's work)

You can then commit/pull/push your new files/edits and once you have finished what you were doing associated with the resequencing project, close the project and switch to the next.

• Remember datasets are not to be stored in the repository

New Repositories

If a repository doesn't exist for what you are doing, in the first instance talk to either Murray or James and we'll help you through the process of creating one