Course Template

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Course Overview

?? This Section is used to build the course website ??

?? What is this course about??

?? Break down of course structure. You can look here for guidance: https://rockefelleruniversity.github.io/Intro_To_R_1Day/??

Course material and exercises are available to view as rendered HTML at https://rockefelleruniversity.github.io/RU_Course_template/. All material is available to download under GPL v2 license.

Course Integrity

This course is compiled automatically on 2026-08-17

The course is tested and available on MacOS, Windows and Ubuntu Linux for R version 4.6.1 (2026-06-24)

The course is also tested against every major R release since 3.5 (3.5 → 4.5) on Linux

Setting up

System Requirements

Install R

R can be installed from the R-project website.

The R website can be found here http://www.r-project.org/. This website has all the latest information about R updates, conferences and installation

You can use this direct links to the install for each major OS:

• Mac
• Windows
• Linux platforms

Install RStudio

RStudio can be installed from the RStudio website.

http://www.rstudio.com/

RStudio can be downloaded for all platforms at the link below

https://rstudio.com/products/rstudio/download/

Install required R packages

R Packages can be installed from the course package or from CRAN/Bioconductor. These commands should be written into the R console. Once R and RStudio is installed, you can copy and paste these install commands into lower left pane of RStudio which should be labelled “Console”. If you run into any errors, do this one line at a time.

From the course package

install.packages('BiocManager')
install.packages('remotes')
BiocManager::install('RockefellerUniversity/RU_course_template')

From CRAN and Bioconductor

install.packages('BiocManager')
BiocManager::install('methods')
BiocManager::install('ggplot2')
BiocManager::install('rmarkdown')
BiocManager::install('knitr')
BiocManager::install('testthat')
BiocManager::install('yaml')

With Docker (reproducible environment)

For an environment matching the one this course was built and tested against, use the Bioconductor Docker image, pinned to the Bioconductor release used at compile time. Docker must be installed; run this in a terminal:

docker run -e PASSWORD=changeme -p 8787:8787 bioconductor/bioconductor_docker:RELEASE_3_23

Then open http://localhost:8787 (username rstudio, password changeme) and install the course in the RStudio console:

install.packages('BiocManager')
BiocManager::install('RockefellerUniversity/RU_course_template')

Download the material

Download the material

The Presentations

?? My course name?? , Session 1

??What am I focusing on in this section. Bullet point lists are good??

• Course content
• Building courses
• Making it look nice

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

?? My course name?? , Session 2

??If you have more sections then do this again. what is session 2 about? keep adding more files if needed??

• Course content
• Building courses
• Making it look nice

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.