CDSB Workshop 2024: Developing R/Bioconductor packages

TIB2024	RMB	NNB	CCG-UNAM

Community of Software Developers in Bioinformatics (CDSB)

We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Developing R/Bioconductor packages as part of the National Bioinformatics Meeting Mexico 2024.

• Level: Intermediate-Advanced.
• Language: Spanish.
• Where: This workshop will be held online on Zoom.
• When: October 28-31 2024, 9:00am - 5:00pm (Mexico City timezone).
• Registration
• Twitter: @CDSBMexico
• Facebook: @CDSBMexico
• GitHub: https://github.com/ComunidadBioInfo/cdsb2024
• Workshop webpage: https://comunidadbioinfo.github.io/cdsb2024
• Calendar

What are you going to learn?

You will learn the crucial steps to develop an R package and some good practices for code generation. With the integration of these tools, you will have the opportunity to create your first package and contribute to the developers community.

Who is it for?

This course is aimed at people who want to learn how to develop packages using R/Bioconductor tools.

Pre-requirements

This workshop is Advanced, so you’ll need some background knowledge:

• Basic knowledge of RStudio:
  • Rscripts creation, RStudio console management, display space management.
• Intermediate knowledge of R:
  • Managing variables, reading files, creating and managing data frames and lists.
  • Generation of graphs.
  • How to install packages from CRAN and Bioconductor.

Technical requirements

• Computer with at least 4Gb of memory.
• Access to a Linux terminal.
• Have R and RStudio installed in their latest version.

Instructors

Instructors

• Dra. Joselyn Cristina Chávez Fuentes: Postdoctoral Fellow at Icahn School of Medicine at Mount Sinai.
• Dra. Mirna Vázquez Rosas Landa: Associate Professor at Instituto de Ciencias de Mar y Limnología de la UNAM.
• Dra. Alejandra Medina Rivera: Associate Professor at Laboratorio Internacional de Investigación de Medicina Genómica, UNAM.
• M.C. Erick Cuevas Fernández: PhD Student at Universidad Nacional Autónoma de México.

Program

Day 1: Project-oriented workflows:

• Introduction to project-oriented workflows.
• Safe paths.
• Good practices for maintaining your workspace.
• Modifying the R startup files.
• New features of RStudio, Quarto.

Day 2: Creating R packages Part I

• Version control with GitHub and RStudio.
• Troubleshooting with Rstudio package versions.
• Infrastructure of an R/Bioconductor package.
• Talk: Converting your analysis workflow into an R/Bioconductor package.
• Documentation of functions.
• Social session: Getting to know the community.

Day 3: Writting R/Bioconductor packages Part II

• Design of tests.
• Vignettes.
• Compilation and installation of packages.
• Collaborative projects Part I.

Day 4: Collaborative projects

• Collaborative projects Part II.
• Projects presentation.
• Closure.

Looking forward to see you!

Organizers

With the support of: