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      Single Cell RNA-Seq Analysis

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Introduction and Lectures
Intro to the Workshop and Core
Support
Schedule
Slack
Cheat Sheets
Software and Links
Scripts
GitHub repository
Biocore website
Prerequisites
CLI
R
Data Reduction
Files and Filetypes
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
Part 1- Create object
Part 2- Filtering
Part 3- Normalization and scaling
Part 4- Dimensionality reduction
Part 5- Clustering and cell type
Part 6- Enrichment and DE
Part 7- Doublet detection
Part 8- Integration

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