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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

script for squidpy analysis

squidpy

script for SCOTIA analysis

scotia

script for cellpose3 analysis

cellpose