Installation Instructions

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:

source("http://bioconductor.org/biocLite.R");
biocLite();

If you are unsure which version you have installed, open R and at the ‘>’ prompt, enter the command:

version

3) A robust text editor.

• For Windows/PC - notepad++
• For Linux - gEdit
• For Mac – TextWrangler

4) A file decompression tool.

• For Windows/PC – 7zip.
• For Linux – gzip.
• For Mac – already there.

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 11).

7) Integrative Genomics Viewer 2.4.x (IGV) - Once java is installed, go to https://software.broadinstitute.org/software/igv/download 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).