Integrated Genome Viewer

Course Overview

Course Integrity

This course is compiled automatically on 2021-03-08

The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.0.3 (2020-10-10)

Overview

This course introduces the use BROAD’s Integrative Genome Viewer (IGV) to display genomics data.

Each section is presented as HTML presentations or single page document. Exercises and answer sheets are included to practice techniques and provide future reference examples.

Course material and exercises are available to view as rendered HTML at http://rockefelleruniversity.github.io/IGV_course/. All material is available to download under GPL v3 license.

Setting up

System Requirements

Install IGV

IGV can be installed from the BROAD website.

https://www.broadinstitute.org/igv/

Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/.

The download links and associated installation instructions for multiple platforms can be found below provided by Revolution Analytics. https://cran.revolutionanalytics.com

We recommend installing R 4.0.3 as this is the version used to compile the course. Direct downloads for R 4.0.3 for the main platforms can be found below:

Install required packages

From the course package

install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/IGV_course',subdir='IGV')

From CRAN and Bioconductor

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('rmarkdown')
BiocManager::install('rio')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')

Download the material

The Presentations

IGV

This course reviews the basics for using the genome browser IGV including:

Navigating around the IGV dashboard
Loading data
Useful tools in IGV

Links to presentations:

The html slide presentation can be found at this link Slide

The single page html presentation can be found at this link Single Page

The code use in the presentations can be found at R code

Getting help

Course help

For advice, help and comments for the material covered in this course please contact us at the issues page associated to this course.

The link to the help pages can be found here

General Bioinformatics support

If you would like contact us about general bioinformatics advice, support or collaboration, please contact us the Bioinformatics Resource Center at brc@rockefeller.edu.