Analysis Using R
Canadian Bioinformatics Workshop
last modified 2023-07-20
Welcome
Welcome to Analysis Using R 2023.
Meet your Faculty
Shraddha Pai
Investigator I, OICR
Assistant Professor, University of Toronto
Dr. Pai integrates genomics and computational methods to advance precision medicine. Her previous work involves DNA methylome-based biomarker discovery in psychosis, and building machine learning algorithms for patient classification from multi-modal data. The Pai Lab at the Ontario Institute for Cancer Research focuses on biomarker discovery for detection, diagnosis and prognosis in brain cancers and other brain-related disorders.
Chaitra Sarathy
Scientific Associate
Princess Margaret Cancer Centre
University Health Network
Dr. Sarathy is a computational biologist with experience in software development. During her PhD, she applied mathematical modelling, network analysis and multi-omics integration to study complex diseases. She has contributed to open-source toolboxes (openCOBRA) and developed softwares (EFMviz & ComMet) to analyse genome-scale metabolic models. She currently works in the Bader lab’s MODiL team (Multi Omics Data Integration and Analysis) and with groups at PMCC, where she develops pipelines to analyse various omics data types and discover new drug targets in cancer.
Delaram Pouyabahar
PhD Candidate
University of Toronto, Donnelly Centre
Delaram is a Ph.D. candidate in Computational Biology at the Molecular Genetics department at UofT. She completed her undergraduate studies at the University of Tehran before joining the Bader lab in Toronto. Her research centers around the development of computational tools to explore sources of variation in single-cell transcriptomics maps, with a particular emphasis on liver biology and transplantation.
Ian Cheong
MSc. Candidate
University of Toronto
Ian is a Master’s level candidate in the Department of Medical Biophysics at the University of Toronto. His thesis work in the Pai lab involves analysis of single-cell transcriptomes to find the link between brain development and the development of childhood brain cancer.
Nia Hughes
Program Manager
Bioinformatics.ca
nia.hughes@oicr.on.ca
Nia is the Program Manager for Bioinformatics.ca, where she coordinates the Canadian Bioinformatics Workshop Series. Prior to starting at the OICR, she completed her M.Sc in Bioinformatics from the University of Guelph in 2020 before working there as a bioinformatician studying epigenetic and transcriptomic patterns across maize varieties.
Pre-workshop Materials and Laptop Setup Instructions
Laptop Setup Instructions
A checklist to setup your laptop can be found here.
Install these tools on your laptop before coming to the workshop:
- R (4.0+) Note: MacBook users with an Apple silicon chip (e.g., M1 or M2) should install the “arm64” version of R, while MacBook users with an Intel chip should install the regular (64-bit) version of R. You can check your laptop’s hardware specifications by clicking the Apple icon (top left corner) > About This Mac and verifying whether the chip is Apple or Intel.
- Rstudio
- Make sure you have a robust internet browser such as Firefox, Safari or Chrome (not Internet Explorer).
- Make sure you have a PDF viewer (e.g. Adobe Acrobat, Preview or similar) or that you can read PDF files in your Web browser.
R packages
pkgList <- c("tidyverse", "clValid","rgl","RColorBrewer","corrplot","ClusterR",
"Rtsne","umap","BiocManager","mlbench","plotrix", "factoextra")
for (cur in pkgList){
message(sprintf("\tChecking for %s ...", cur))
if (!requireNamespace(cur, quietly = TRUE)) install.packages(cur)
}## Checking for tidyverse ...## Checking for clValid ...## Checking for rgl ...## Checking for RColorBrewer ...## Checking for corrplot ...## Checking for ClusterR ...## Checking for Rtsne ...## Checking for umap ...## Checking for BiocManager ...## Checking for mlbench ...## Checking for plotrix ...## Checking for factoextra ...if (!requireNamespace("edgeR", quietly = TRUE)) BiocManager::install("edgeR")
if (!requireNamespace("curatedTCGAData", quietly = TRUE)) BiocManager::install("curatedTCGAData")We are going to use titanic.csv in Module 3.
Download the dataset here and copy it into your working directory.