Upcoming Data Analysis Support Group Sessions
Come and join our Data Analysis Support Group sessions! These are bi-weekly meetings where trainees and other researchers of all levels of experience can learn tools for data analysis and get coding help from experienced tutors. Sessions will alternate between open, informal help sessions where researchers can ask questions and troubleshoot their work, and guided work-alongs where volunteers will teach participants how to use specific useful tools and packages in R and other languages. These sessions are aimed to support BCCHR researchers using programming for data analysis by providing a relaxed, social setting to come together with peers to work through problems and learn new skills. Please install RStudio before arriving (if applicable to the tutorial)!
Information will be sent out via our mailing list and/or Research Education closer to scheduled session dates. To join our mailing list, use the form at the "Contact Us" page.
September 28, 2021 (1-2pm): Integration of Epigenetic and Transcriptional Data and Network Analysis with SMITE
Who should attend this workshop?
- Trainees who are interested in learning about multi-omic integration approaches, considerations for choosing an approach, and how to interpret results
- Trainees who work with either epigenetic data and/or gene expression data. We will be focusing on DNA methylation and RNA-seq data for this workshop, although SMITE can also be used to integrate gene expression with other ‘omics (e.g. ChIP-seq, DNA hydroxymethylation).
What level of coding/R experience is required for this workshop?
This is an intermediate-level tutorial. Participants should have some prior experience in R, including familiarity with the console and environment, working directory, running code, and saving objects. Prior knowledge of statistical methods for analyzing genome-wide DNA methylation and gene expression data is an asset, but not required, as we’ll be working with statistics from data that has already been analyzed.
Do I need to do anything before attending the tutorial?
Yes, please see below for prerequisites:
1. Install RStudio if you have not already: https://rstudio.com/products/rstudio/download/#download
2. Download the following files from our GitHub repository and save into a folder to use as your working directory during the tutorial: “SMITE_Practicum_092021.Rmd” (we will work through this file in RStudio), “LUHMES_DNAm.csv”, “LUHMES_expr.csv”, “LUHMES_spinglass.RData”, “plotModule2.R”, “annotateModification2.R”, “hg19_bed.RData”
3. Install the following R packages (open RStudio and copy and paste the following commands into the console):
BiocManager::install(c(“SMITE”, “dplyr”, “reshape2”, “ggplot2”))
What if I'm interested in learning about this but I can't make it today?
We always post our tutorial materials on our GitHub repository after the workshop is finished! Feel free to download the Rmd file and work through it at your own pace. If you have questions, join our Slack workspace and you can chat with our TOG tutors at any time.
We hope to see you there! Feel free to email us at firstname.lastname@example.org or post on our Slack channel #tog-community with any questions.
Past Guided Data Analysis Support Group Sessions
All of our past tutorial material is posted on our GitHub repository. Take a look through the below links to find code you can work along with if you missed a tutorial!
July 25, 2019
Victor Yuan gave a great ggplot2 tutorial to kick off our R Study Group series! In case you missed it or want to revisit his material, you can find the code for the tutorial here.
September 5, 2019
Giulia Del Gobbo gave a fantastic introduction to using Rmarkdown and the Rstudio Environment. All of Giulia's code for the tutorial are here.
October 3, 2019
Victor Yuan came back this week with another tidyverse tutorial. This time, he covered data manipulation in dplyr. You can find his code and a walk-through of his lesson here.
October 31, 2019
Amy Inkster developed a spooky Halloween tutorial for those who are complete beginners in R! Click here to see her presentation "R: It's Not So Scary!"
November 28, 2019
Will Casazza lead a tutorial on using version control with Git and Github. A great walk-through of his material (based on the UBC STAT 540 course) can be found here.
April 16, 2020
Dr. Mike Irvine's GitHub example material from the tutorial "Writing Tests and Validating Data in R" can be found here, and a video recording of the session can be found here (accessible to BCCHR members only).
May 28, 2020
The code from Christina Michalski's tutorial on PCA plots and heat maps in R can be found on our GitHub page.
July 9, 2020
Click here to find Victor's intro to ggplot2 tutorial materials!
July 23, 2020
The material for Almas's tutorial on data manipulation using dplyr can be found here.
October 29, 2020
Click here for the content of our EWAS series part 1, "Working with data from GEO and differential DNA methylation analysis in limma" (Will Cassazza and Sam Schaffner).
November 26, 2020
The content of our EWAS series part 2, "Gene ontology enrichment with gprofiler2", is available on our GitHub.
What topics would you like to see covered?
Do you have any suggestions for future guided study group topics? Is there a specific R package or data analysis strategy you would like a tutorial on? Click the button below to go to our Contact page and send us a message with your ideas!