Last updated: 2023-12-05
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Knit directory: mi_spatialomics/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 67e546d | FloWuenne | 2023-07-23 | Build site. |
| html | 3b5ca40 | FloWuenne | 2023-06-12 | Added code for supplementary Figures. |
| html | 51754b9 | FloWuenne | 2023-06-12 | Build site. |
| html | 09358ac | FloWuenne | 2023-06-12 | Build site. |
| 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. |
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 interface with the following command, which will download
all of the raw data.
`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.gitImaging 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 : ./pipeline_configs
For more details on data processing, go to Data processing.
All raw images and processed data is available from Synapse: Highly-multiplexed imaging of immune cell infiltration routes in myocardial infarction.
Please cite our preprint if using any of the data used in study: