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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

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By Eleanor C. Williams