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Class Photo
Laptop Setup Instructions
1) Install the most recent version of R for your operating system by following the links from http://www.r-project.org/
2) Download and install the most recent version of R Studio desktop from http://www.rstudio.com/
3) Make sure you have a robust internet browser such as Firefox, Safari or Chrome (not Internet Explorer).
4) Make sure you have a PDF viewer (e.g. Adobe Acrobat, Preview or similar) or that you can read PDF files in your Web browser.
5) Create a project directory for data files and source code for this workshop.
Difference Between R and RStudio
RStudio doesn’t know where libraries are installed, when they are not installed through the RStudio package manager. To tell RStudio the location, you can define the path in a startup file. Create a file called .Renviron . Inside there:
R_LIBS=<R Library Path of other installed packages>
That was the problem when students installed things in RStudio at the command line using the R command install.package().
… or you could use the package manger to install libraries.
Syntax highlighting
… of scripts in the R editor does not seem to work under Windows. If you want highlighted syntax, use RStudio instead.
Helpful Materials
YouTube Playlist for Recorded Lectures
Day 1
Welcome
Ann Meyer
Module 1: The R Environment
Boris Steipe
Scripts:
Data:
- Fig_3-CharacteristicGenes.txt
-
Supplementary data: Table_S3.xls
Practical:
- Using Projects with R Studio
- Software Carpentry
- Best Practices for Scientific Computing
-
Resources:
Helpful Links:
- The R help mailing list
- Rseek: the specialized search engine for R topics
- R questions on stackoverflow
- The Comprehensive R Archive Network CRAN
- The CRAN task-view collection
- Bioconductor task views
Module 2: Programming Basics
Boris Steipe
Scripts:
Module 3: Using R for Data Analysis
Boris Steipe
Resources:
Practical: