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2018_scWorkshop

Participant Connection Info

Docker Container

All practicals in this workshop can be ran in the following docker instance. https://hub.docker.com/r/trinityctat/2018_bern . The easiest way to use this container is to install Docker on your machine and pull the instance with the command docker pull trinityctat/2018_bern:latest

Data can be found Here . You will need to uncompress it to use it in the practicals.

To start the docker instance you have to map the image to your browser. Here is an example command; after this command go in your browser and access http://localhost:10000 (user and password are both "training").

docker run --rm -ti -v /path/local/data/bern_sc_workshop_2018:/home/training -p 10000:8787 trinityctat/2018_bern:latest

Agenda

For more detail please click on links or go to this repo's wiki.

Day 1

9:15 Welcome and Introductions

9:30 What is scRNA-Seq and how it compares to population

10:30 Break

11:00 What is scRNA-Seq and how it compares to population, continued

11:30 Intro to R and RStudio

12:00 Lunch

13:00 Intro to R and RStudio, cont

13:30 Presentation: Single Cell QC Metrics

15:00 Break

15:30 Practical: Single Cell QC Metrics

16:30 Wrap-up questions

Day 2

9:15 Practical continued: Single Cell QC Metrics

9:45 Review and questions

10:00 Presentation: Clustering and Differential Expression

11:00 Coffee Break

11:30 Practical: Clustering and Differential Expression

12:00 Lunch

13:00 Practical: Clustering and Differential Expression continued

13:30 Presentation: Trajectories

14:00 Practical: Trajectories

14:45 Break

14:30 Presentation: Emerging trends and Projects in the scGenomics Community

15:30 Demo: Collaborative Spaces for scRNA-Seq

16:00 Wrap up questions

16:30 Practical: Uploading Studies in the scPortal