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      Adv Topics in scRNA-Seq: Trajectory and Velocity Analysis

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Introduction and Lectures
Intro to the Workshop and Core
Support
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
More Materials - Intro CLI
More Materials - Intro R
Velocity Analysis
Velocity data reduction
Prepare for Velocity analysis
Velocity data analysis
Monocle Trajectory Analysis
Prepare for Monocle
Monocle
ETC
Closing thoughts
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