1) Install latest version of R which can be downloaded from http://probability.ca/cran/.
1b) Download and install the most recent version of R Studio desktop. If prompted to install git, select yes.
2) Install the BioConductor core packages. If you have installed R version 3.5.0 or higher, open R and at the ‘>’ prompt, paste the commands:
install.packages("BiocManager"); library(BiocManager); BiocManager::install();
If you already have an older version of R installed (3.4.4 or lower), open R and at the ‘>’ prompt, paste the commands:
If you are unsure which version you have installed, open R and at the ‘>’ prompt, enter the command:
3) A robust text editor.
4) A file decompression tool.
5) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).
6) Java -The visualization program that we will be using (IGV) requires Java. Check if you have Java installed: https://www.java.com/verify/ and download Java if you do not have it installed (You need Java 8. Do NOT install Java 10).
7) Integrative Genomics Viewer 2.4 (IGV) - Once java is installed, go to http://www.broadinstitute.org/igv/ and register in order to get access to the downloads page. Once you have gained access to the download page, click on the appropriate launch button that matches your computer’s operating system
8) SSH client - Mac and Linux users already have a command line ssh program that can be run from the terminal. For Windows users, please download PuTTY.
9) SCP/SFTP client - We will be moving data from the servers to the student laptops for visualization. Mac and Linux users already have a command line scp and sftp program. For Windows users, please install WinSCP.
10) A PDF viewer (Adobe Acrobat or equivalent).