- Make sure you can connect to uppmax using a terminal, all participants should have recieved login instructions. If you use a pc we recommend MobaXterm (http://mobaxterm.mobatek.net).
- If you still feel uncertain how to work in a terminal please take time to do the first three parts in the “Unix tutorial for beginners” that can be found here http://www.ee.surrey.ac.uk/Teaching/Unix/ before the course starts. Otherwise you will not be able to take in the practical parts.
- Make sure that you can read and write in the course folder by creating a file with your name in the /proj/g2017018/completed folder. We will check before the course that all students have logged in and done this, so do not forget!
- Install R on your own computer (the latest version), instructions can be found here.
- Install Rstudio on your own computer to run all your commands (This is optional). Rstudio is a very powerful GUI for structuring your R code in a good way.
- If you feel that you need to touch up on your R-skills before the course start, we recommend that you go through some basic tutorials before the course starts. A list of useful tutorials can be found here.
- In R install the programs listed below. We will work with several R programs during the course and it takes a while to install so if you can do it before you will not have to waste time installing during the exercise time.
- SCDE package - website, bioconductor
- Scater package - website, bioconductor
- SC3 package - website, bioconductor
- SCRAN package - website, bioconductor
- Seurat package - website
- MAST package - website, bioconductor
- Monocle package - website, bioconductor
OBS! If you run in to trouble during installations, please have a look at the troubleshooting pages for installations that most of the packages have. If you still do not succeed in installing them, please email to Åsa Björklund (asa.bjorklund at scilifelab dot se) and she will try to help you out if possible.