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Update integration.md
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giuliaelgarcia authored Apr 26, 2024
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Expand Up @@ -4,7 +4,7 @@ The panpipes integration pipeline implements a variety of tools to batch correct

![integration_flowchart](../img/integration_coloured.drawio.png)

The flowchart indicates which tools are available for each modality out of RNA (also referred to as GEX), PROT (also referred to as ADT) and ATAC. You can run as many of these tools as you choose and then you can run `panpipes integration make merge_integration` to create a final object containing one reduced dimension representation and one nearest neighbor graph per modality. This can be used as input to the clustering pipeline.
The flowchart indicates which tools are available for each modality out of RNA (also referred to as GEX), PROT (also referred to as ADT) and ATAC. You can run as many of these tools as you choose, including a version with no correction and, then you can run `panpipes integration make merge_integration` to create a final object containing one reduced dimension representation and one nearest neighbor graph per modality. This can be used as input to the clustering pipeline.

## Steps to run

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