R/Bioconductor Watch Party

#BioC23 @R-Ladies Rome
Department of Statistics - La Sapienza
August 28, 2023

What is Bioconductor?

Bioconductor is a collaborative project that started in 2001 to create software for computational biology and bioinformatics. Its main goal is to develop tools for analyzing and understanding large biological datasets from experiments. These tools include statistical analysis, visualization, and making results reproducible.

How many packages does the current release of the Bioconductor project include?

https://carpentries-incubator.github.io/bioc-project/
Types N
Software 2230
Annotation 912
Experiment 419
Workflow 27
Total 3588

How to get started with Bioconductor?

install.packages("BiocManager")
BiocManager::install(version = "3.17") 


BiocManager::install("pkg-name")
library("pkg-name")

Bioconductor Conference 2023

Agenda

Watch party

  • Keynote (~ 20min)
  • Short talks (3 X ~ 10min)
  • Workshops (2 X ~ 20min)

Keynote

Reproducible Manuscripts with Quarto by J.J. Allaire - CEO of POSIT PBC - length 23:18

Short talks

  • Spatial Transcriptomics

{SPAMMER}: Spatial Analysis of Multi-omics Measurements in R by Harkirat Kaur Sohi - Pactific Northwest - length 11:42

Short talks

  • Infrastructure

{rworkflows}: taming the Wild West of R packages by Brian Schilder - Imperial College London, UK - length 10:29

rOpenSci 👉 https://ropensci.org/ provides Mentorships opportunities: https://ropensci.org/champions/

Short talks

  • Single-cell

Model-based Dimensionality Reduction for Single-cell RNA-seq with Generalized Bilinear Models by Phillip Nicol - Harvard Cancer - length 08:41

Workshops

  • Introduction to R/Galaxi

Log in: https://workshop.bioconductor.org/

  • Epidemiology for Bioinformaticians by Chloe Anya Mirzayi - CUNY School of Public Health - length 26:09

Material: https://rpubs.com/cmirzayi/epi4bio2023

Workshops

  • R/Galaxi hands-on

Log in: https://workshop.bioconductor.org/

  • Differential Expression Analysis using Limma and qsvaR by Hedia Tnani - Johns Hopkins - Liber Institute for Brain Development - length 19:13

Bonus

  • Tidy genomic and transcriptomic analyses, a {tidyverse} framework for genomics analysis by Stefano Mangiola and Michael Love - WEHI: Walter and Eliza Hall Institute of Medical Research

Webcomic xkcd

Conclusions

Thank you for joining us at this watch party! 🎉 We delved into the latest developments in computational biology and bioinformatics. We’ve explored the remarkable growth of Bioconductor, reflecting the dynamic nature of this field.

How can I contribute?

Become an Instructor: Bioconductor Carpentries global teaching program

R-Ladies Rome sponsored by RConsortium