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Knit directory: mi_spatialomics/
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| Rmd | 14c162a | FloWuenne | 2024-08-07 | Added preprint information to Home. |
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| Rmd | 56559c7 | FloWuenne | 2024-03-21 | Cleaned up repository. |
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| html | 2dcd178 | FloWuenne | 2023-12-06 | wflow_publish("*") |
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| html | 3b5ca40 | FloWuenne | 2023-06-12 | Added code for supplementary Figures. |
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| Rmd | 576e518 | FloWuenne | 2023-06-12 | wflow_publish("analysis/index.Rmd") |
| html | 8ef6779 | FloWuenne | 2023-06-12 | Build site. |
| Rmd | 0c01112 | FloWuenne | 2023-06-12 | wflow_publish(c("analysis/about.Rmd", "analysis/index.Rmd", "analysis/license.Rmd")) |
| Rmd | 9e88e37 | FloWuenne | 2023-06-12 | Start workflowr project. |
This repository contains the code required to reproduce the results from the manuscript ‘Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration’. The repository is organized as follows:
All scripts in this repository assume that this repository is in the
same parent folder as the /data directory, containing all
the data on Synapse. Data directory structure can be set up using the
Synapse command-line interface with the following command, which will
download all of the raw data to your local drive.
`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/FloWuenne/mi_spatialomics.gitImaging data in this study was processed using Nextflow pipelines
designed for each specific data type (nf-core/molkart -> Molecular
Cartography, MCMICRO -> SeqIF). 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 : ./pipeline_configs
For more details on data processing, go to Data processing.
All raw images and processed data is available from Synapse: Spatial omics of acute myocardial infarction reveals immune cell infiltration via the endocardial layer.
Please cite our preprint if you are using any of the data produced in this study:
Spatial omics of acute myocardial infarction reveals a novel mode of immune cell infiltration