Last updated: 2023-06-12

Checks: 2 0

Knit directory: mi_spatialomics/

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Rmd	9e88e37	FloWuenne	2023-06-12	Start workflowr project.

Introduction

Data setup

All scripts in this repository assume that this repository is in the same folder as the /data directory, containing all the data on Synapse. Data directory structure can be set up using the Synapse command-line interace with the following command

`synapse get -r syn51449054 `

For more options to download the data within Synapse, you can select Download Options in the Synapse project and check out Programmatic options. This will allow to also download the data directly using R and Python.

You can then clone this repository alongside the data repository from Synapse:

git clone https://github.com/SchapiroLabor/MI_infiltration_imaging.git

Data processing

Pipelines used to process the imaging data

Imaging data in this study was processed using nextflow based pipelines designed for the specific data type. Links to the original pipeline repositories is provided below. Config files and specifications for running each pipeline to process the data is provided in this repository under : ./

Processing of Molecular Cartography was done using nf-MolCart.
Processing of SeqIF (Lunaphore COMET) data was done using MCMICRO.

For more details on data processing, go to Data processing.

Data availability

All raw images and processed data is available from Synapse: Highly-multiplexed imaging of immune cell infiltration routes in myocardial infarction.

Citation

Please cite our preprint if using any of the data used in study: