Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

Department of Statistics, University of Oxford

Sep 2-3, 2024

9:00 am - 5:00 pm ET

Instructors: Fabricio Almeida-Silva, Robert Ivanek

Helpers: Maria Doyle

General Information

Bioconductor Carpentries develops and teaches workshops on the fundamental data skills needed to conduct omics data analysis. Its target audience is experimental researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Good Enough Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. This lesson assumes you have a working knowledge of R and some previous exposure to RStudio. The following prerequisites apply:

Familiarity with R/Bioconductor, such as taught in Introduction to data analysis with R and Bioconductor lesson.
Familiarity with statistical hypothesis testing, such as Chapter 6 of Modern Statistics for Modern Biology book by Holmes and Huber.
Familiarity with the biology of gene expression and RNA-seq, such as RNA sequencing: the teenage years manuscript by Hadfield et.al.

Learner profiles of hypothetical attendees of the RNA-Seq workshop can be found on this page.

Participants should bring their own laptops and plan to participate actively.

Where: 24-29 St Giles, Oxford, United Kingdom. Get directions with OpenStreetMap or Google Maps.

When: Sep 2-3, 2024. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they are able to install software on (i.e., administrative privileges). They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

The room is wheelchair / scooter accessible.
Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email maria.doyle [at] ul.ie , fabricio.almeidasilva [at] psb.vib-ugent.be or robert.ivanek [at] unibas.ch for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Registration

This is an in-person workshop only. Virtual attendance is not possible.

Cost: 100 pounds (covers cost of workshop and tea/coffee breaks)
Places are limited to 25 participants, on a first-come first-serve basis.
A confirmation email with payment detail will be sent on a weekly basis from 15 July onwards. Registration will be final after payment. We will not be able to refund the registration fees.
To register, please fill out the application form.

Code of Conduct

Everyone who participates in Bioconductor activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Schedule

Day 1

Morning	Workshop Overview
	Introduction to RNA-seq
	RStudio Project and Experimental data
Afternoon	Importing and annotating quantified data into R
	Exploratory analysis and quality control
Evening	END

Day 2

Morning	Differential expression analysis
	Extra exploration of design matrices
Afternoon	Gene set enrichment analysis
	Next steps
	END

Setup

To participate in a Bioconductor workshop workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The setup instructions for the R/Bioconductor RNAseq workshop can be found at the workshop overview site.