Summary and Schedule

This is a new lesson built with the Melbourne Bioinformatics fork of the Carpentries Workbench.

For more information on Melbourne Bioinformatics, please see our official page and our tutorial collection. If you would like to attend one of our workshops, please follow our Eventbrite page, where you can get notifications and register for upcoming workshops.

	Setup Instructions	Download files required for the lesson
Duration: 00h 00m	1. Using RMarkdown	How do you write a lesson using R Markdown and sandpaper?
Duration: 00h 12m	2. Python with reticulate	How do I run Python code in a Workbench lesson? How do I declare the Python packages an episode needs? How do I pass objects between R and Python?
Duration: 00h 32m	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.

Please follow the steps below and install the required software before the scheduled workshop.

RStudio Setup

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We use RStudio for coding in R.

Click here and follow the instructions to install RStudio Desktop in your system.

Discussion

R packages

Most workshops using R will require the installation of specific packages. Make sure to check in advance with the workshop organisers what packages need to be installed.

You can install packages from CRAN using:

R

install.packages("package_name")

If your package is in a different R repository, such as Bioconductor or GitHub, you may need the BiocManager or devtools packages to install them. To install BiocManager:

R

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

For devtools, you can simply do:

R

install.packages("devtools")

You can then install packages directly from GitHub with:

R

devtools::install_github("username/reponame")