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      Spatial Transcriptomics 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
Spatial Transcriptomics
Technologies
Introduction to Data
Part 0- Prepare R Env
Part 1- Data Exploration
Part 2- Clustering
Part 3- Cell type
Part 4- Niche
Part 5- NicheDE
Part 6- CCC
Part 7- Cell Segmmentation

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