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MAGPIE Pipeline Documentation
Intro
Pipeline Overview
Setup Instructions
MAGPIE directory structure
Pipeline outputs
Pipeline Outputs
Individual pipeline steps
Magpie shiny app for landmark selection
Running the snakemake pipeline
Snakemake Rule 1: Transform coordinates to match between modalities
Snakemake Rule 2: Create spaceranger object
Snakemake Rule 3: Match observations between modalities
Tutorial
MAGPIE tutorial on SMA mouse brain sample
Index
