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      Introduction to 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
Biology at True Resolution - Introduction to Single Cell and Visium Spatial Solutions
Visium Spatial Protocols - Tissue Preparation Guide
Support
Using Slack in this workshop
Using Zoom in this workshop
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
Project setup
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 (extra)
Shiny App on AWS (extra)
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. 10x Cell Ranger
  2. Awesome Singlecell
  3. Satija Lab - how many cells
  4. Satija Lab - cost per cell