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      Single Cell RNA-Seq Analysis

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Talk by Diana Burkhat-Waco from 10x Genomics
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CLI
R
Data Reduction
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Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Shiny App Data Explore
Shiny App on AWS (extra)
ETC
Closing thoughts
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Biocore website

Starting a Shiny Server Instance from the Preconfigured Image

Keith Mitchell (kgmitchell@ucdavis.edu)


Visit here to see how the instance was initially configured:

Setting up an AWS account for yourself

How to prepare the instance for a client:

  1. Go to the AWS AMI’s (Amazon Machine Images). Select the Rshiny Server Image. Go to Actions>Launch
  2. Next Choose and Instance Type. This will vary in general based on the size of the data you are attempting to analyze. In general it is advised to start with a smaller instance and then move up from there if necessary.
  3. Next Configure the Instance Details. The main step here is to set the “Auto-assign Public IP” to enable.
  4. Keep clicking the bottom right button, “Next: Configure Security Group” until you get to “Step 6: Configure Security Group”
  5. At step 6, select the Rshiny App security group.
  6. Finally launch the instance. (Bottom right hand quarter)
  7. Select an existing key pair or create a new key pair is the final step for starting the instance. Choose “Create a new key pair” and give the key a useful name, here we will use “tutorial”.
  8. Move the downloaded key to ~/.ssh/ via mv ~/Downloads/tutorial.pem ~/.ssh/
  9. chmod 700 ~/.ssh/tutorial.pem
  10. Get the connection to the instance seen highlighted below “ec2-…….amazonaws.com”
  11. Run the following command to upload the “experiment_merged.Rdata” object to the app:
    • scp -i ~/.ssh/tutorial.pem ec2-54-219-166-77.us-west-1.compute.amazonaws.com:/srv/shiny-server/scRNA_shiny_app/ ~/Desktop/experiment_merged.rds
  12. Replace the green section with your Public IV4 DNS address from the instance that was created and used in the previous step.
    • http://ec2-54-219-166-77.us-west-1.compute.amazonaws.com:3838/scRNA_shiny_app/
  13. If there are problems with this link do the following:
    • SSH into the server.
      • ssh -i ~/.ssh/tutorial.key ec2-54-219-166-77.us-west-1.compute.amazonaws.com
    • Restart the shiny service.
      • sudo systemctl restart shiny-server.service
  14. Memory issues?
    • The default memory limit for R on the instance has caused me some problems in the app and it can be tricky to debug.
    • The following link was a solution for this issue but feel free to reach out if you have any other issues in regards to this.
      • https://stackoverflow.com/questions/1395229/increasing-or-decreasing-the-memory-available-to-r-processes
      • You can increase the default using this command, memory.limit(size=2500), where the size is in MB.
      • Or you can check the amount of available memory using memory.limit()