Yeasts (saccharomyces cerevisiae) are used in the production of some of our diet's most cherished choices such as bread (not mentioning wine and beer). There are many other biotechnology applications that use yeast, some of which include complex pharmaceuticals production. Yeasts are also great model organisms because of their simple and small genome consisting of approximately 6000 genes. Being single celled organisms also make them great for transcriptome analyses as gene expression is homogenous. As part of our Vancouver-based hackathon (hackseq19) project (October 18 to 20, 2019) we will be examining a yeast transcriptome dataset. In this data, a number of yeast strains have been treated with various stimuli, and gene expression changes are the readout. Expression is normalized to Transcript Per Million (TPM). As a team, we will be cleaning, analyzing, and communicating the results of our explorations through clear documentation of procedures and an interactive application.
The data in this project includes gene expression values for 92 yeast strains treated with various stimuli. RNA expression levels are normalized to TPM (transcripts per million), following a default normalization procedure. Data is stored in data folder.
- The
SC_expression.csvfile contains gene expression of yeast strains in the experiments. - The
labels.csvfiles pertain to gene validation status and molecular function (MF), cellular component (CC), and biological processes (BP) of those genes. - The
conditions_annotation.csvfile explain the yeast strains and experimental conditions.
This project is inspired by the yeast-omics dataset shared as a kaggle competition, and the original data can be found here.
The goal of this project is to unravel the genetic mechanisms involved in yeast stress adaptation through building a visualization platform (e.g. shiny application) that allows scientists to explore the data interactively.
The tasks we will attempt in the hackathon include:
- Perform unsupervised and supervised clustering of expression data
- Perform gene set enrichment analyses (GSEA, ReactomePA)
- Create visualizations of results (heatmaps, barplots, etc.)
- Phylogenetic/Taxonomic trees for yeast strains
You will need an introductory knowledge of R, RNA expression analysis workflows, design thinking, and coding skills. Coding in R (or Python) and basic knowledge of git/github is an asset. Team communications will happen in person and in slack.
Please have the latest versions of R and R Bioconductor installed on your laptop prior to the workshop. RStudio (the free version) is highly recommended as well, since we will be teaching in this environment.
- Introduction to Data Science with R
- RNAseq Analysis tutorials in R and Differential expression Analysis
- Mastering Shiny
- Data Manipulation and Visualization using R
- RNAseq data analysis workflow
- Setting up reproducible projects in R and package management for reproducible R code and reproducibility good practices
- Yeast pathway analysis in R
- Additional resources from UCSF Data Science Initiative
- Package development, maintenance, documentation, and peer-review
- Shiny Apps for Transcriptome Visualizations
- RNAseq Shiny app options
| Time | Event | Location |
|---|---|---|
| 8:30 AM | Coffee and snacks | LSI, UBC |
| 9:00 AM | hackseq kickoff | LSI, UBC |
| 9:30 AM | Team meet + hacking | LSI, UBC |
| 11:30 AM | Intro to Git/Github Workshop (Optional) | room 1330 |
| 1:00 PM | Lunch | LSI, UBC |
| 2:00 PM | Continue hacking | LSI, UBC |
| 5:00 PM | Team Scrum + wrap-up | LSI, UBC |
| 5:30 PM | Unofficial Evening Social | The Gallery, UBC |
| Time | Event | Location |
|---|---|---|
| 8:30 AM | Coffee and snacks | LSI, UBC |
| 9:00 AM | Hacking! | LSI, UBC |
| 12:00 PM | Lunch | LSI, UBC |
| 2:00 PM | Hacking… | LSI, UBC |
| 5:00 PM | Team Scrum + wrap-up | LSI, UBC |
| 5:30 PM | hackseq Evening Social | BierCraft, UBC |
| Time | Event | Location |
|---|---|---|
| 8:30 AM | Coffee and snacks | LSI, UBC |
| 9:00 AM | Red-eye hacking | LSI, UBC |
| 12:00 PM | Lunch | LSI, UBC |
| 2:00 PM | Desperate bug-fix time | LSI, UBC |
| 3:30 PM | Team Project Presentations | LSI, UBC |
| 4:30 PM | Coffee Break | LSI, UBC |
| 4:30 PM | Abcellera talk | LSI, UBC |
| 5:00 PM | hackseq19 wrap-up | LSI, UBC |
Noushin Nabavi, Matthew Emery, Alex Morin, Zuhaib Ahmed, Casey Engstrom, Sedat Demiriz, Shinta Thio, Saelin Bjornson