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      Advanced Single Cell RNA-Seq Workshop

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
Single Cell Sample Preparation - Dr. Diana Burkart-Waco
Support
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Data Reduction
Generating Expression Matrices
Expression project setup
Preprocessing reads with HTStream
Generating Expression Tables
VDJ T cell and B cell
Velocity analysis
Data analysis
scRNA analysis prepare
Mapping Comparison
Anchoring (Comparison dataset)
Shiny App Install/Overview
App Practical Usage
AWS Hosted App (Optional)
Monocle
VDJ T cell and B cell analysis
Velocity analysis
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website

Software and Links

Linux Terminal:

  1. Shell for Windows 10 tutorial
  2. Enable SSH tutorial OR
  3. MobaXterm
  4. PuTTY

R and RStudio

  1. R project
  2. RStudio Desktop Also see this link if you have trouble installing under Ubuntu
  3. Seurat

Single cell Resources

  1. Awesome Singlecell
  2. Satija Lab - how many cells
  3. Satija Lab - cost per cell

Software

  1. HTStream
  2. 10x CellRanger
  3. Star
  4. Salmon