scRNA-seq Workshop

Posted on Monday, April 27, 2020

WORKSHOP DETAILS

Topic: scRNA-seq Workshop

Time: Apr 27, 2020 09:30 AM Eastern Time (US and Canada) #workshop will start at 10:00

 

Join Zoom Meeting

https://zoom.us/j/97416939217?pwd=N25aVnorMFlrMlV4b3JmMzluQWs0Zz09

Meeting ID: 974 1693 9217

Password: 168056

 

ROUGH WORKSHOP ITINERARY

9:30-10:00

Sign in


10:00 - 12:00

Introduction of scRNA-seq methodologies and anlaysis

Basic introduction to R and RStudio

Download data and dependencies


12:00-1:00

Lunch break

Troubleshoot installation issues

 

1:00-2:30

Data preprocessing & quality control

Normalization

Dimensionality reduction


2:30-3:00

Coffee/Beer/Troubleshooting break

Walk my dog quickly


3:00-4:00

Visualization

Intro to downstream analysis approaches

 

4:00-5:00

Optional happy hour hangout

Loose ends & questions

Note from David Cook, PhD Candidate (Vanderhyden Lab) I'm hoping to make a video recording of the workshop available afterwards. All code and data used will be hosted on a public Github repo.

 

RESOURCES

R For Data Science - https://r4ds.had.co.nz. Free online book to get started with data wrangling and visualization using R. Written by Hadley Wickham, who developed some of the most popular R packages.


Seurat's "Guided Tutorial" - https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html. A well-documented introduction to scRNA-seq analysis using Seurat, which is probably the most common tool used currently. My tutorial will be based on this.


Ming Tang's collection of scRNA-seq notes - https://github.com/crazyhottommy/scRNAseq-analysis-notes. Ming has been putting together a massive collection of papers/blogs/resources related to scRNA-seq analysis. This is a reeeally good resource.

To join Ottawa CompBio Slack

https://join.slack.com/t/ottawacompbio/shared_invite/zt-dsmwsqbl-TrZz5qF5UvhNPM9F5sIo~w

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