CDSB Workshop 2023: Writting R/Bioconductor packages for scRNAseq analysis.

TIB2023	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 Writting R/Bioconductor packages for scRNAseq analysis as part of the National Bioinformatics Meeting Mexico 2023.

• Level: Intermediate-Advanced.
• Language: Spanish.
• Where: This workshop will be held online on Zoom.
• When: 07-11 August 2023, 9:00am - 5:00pm (Mexico City timezone).
• Registration
• Twitter: @CDSBMexico
• Facebook: @CDSBMexico
• GitHub: https://github.com/ComunidadBioInfo/cdsb2023
• Workshop webpage: https://comunidadbioinfo.github.io/cdsb2023
• Calendar

What are you going to learn?

In recent years, the generation of scRNAseq data has become very important in biomedical research; however, the tools needed for its analysis are still under development.

In this workshop, we will review the existing statistical tools to analyze scRNAseq data using Bioconductor, how to document your analysis and check some tools for interpreting results.

At the same time, 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 packets to analyze scRNAseq data using R/Bioconductor tools.

Pre-requirements

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

• Basic knowledge of RNAseq.
• 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 8Gb 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. Yalbi Balderas Martínez: Investigator at Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas.
• Dr. Leonardo Collado Torres: Investigator at Lieber Institute for Brain Development.
• M.C. Erick Cuevas Fernández: PhD Student at Universidad Nacional Autónoma de México.
• 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.

Invited speakers

• Dra. Evelia Lorena Coss Navarrete
• M.C. José Antonio Ovando Ricárdez
• M.C. Andrés Arredondo Cruz

TAs

• M. C. Diego Ramírez
• M. C. Luis Alberto Meza

Program

Day 1: scRNAseq analysis workflow Part I

• Presentation of the CDSB.
• Structure and importing of data.
• Quality control.
• Normalization.

Day 2: scRNAseq analysis workflow Part II

• Selection of highly variable genes.
• Dimension reduction.
• Clustering.
• Marker genes.
• Annotation of cellular types.

Day 3: Writting R/Bioconductor packages Part I

• New features of RStudio, Quarto.
• 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 4: Writting R/Bioconductor packages Part II

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

Day 5: Collaborative projects

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

Looking forward to see you!

Organizers

With the support of: