Monday, May 1, 2017

JAX computational genomics tools

On the academic side:

We will be using a number of genomic analysis software packages/tools. Please try to download and install the tools/programs listed below (IGV, R/RStudio and Python).  Ada Zhan (cc’ed here) can assist you with installation questions. We will also be able to provide support on the first day of the course. We will use a cloud computing environment (web-based) but you will get information on that platform just before the course.

If you do not have a laptop at your disposal please alert me ASAP so that we can prepare a machine for your use.

Please install the following:

Integrative Genomics Viewer: (IGV) (Broad Institute)

Please go to the Broad institute website here and download the IGV version for your Mac or PC.


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio   To install on:


Mac OS X:


Python:  To set  up Python:


Mac OS X


  1. Download the installer that matches your operating system and save it in your home folder. Download the default Python 3 installer.
  2. Open a terminal window.
  3. Type
bash Anaconda-
  1. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

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