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Must use "safe" titles, consistent formatting
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hexylena committed Apr 5, 2024
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Expand Up @@ -64,27 +64,29 @@ To start, let's get our dataset loaded into Galaxy.

{% include _includes/cyoa-choices.html option1='EBI Data Retrieval' option2='Importing from a history' option3='Uploading from Zenodo' default='EBI Data Retrieval' text="There are multiple ways in which to collect the data for this tutorial. I find it easiest to do so via the EBI Data Retrieval." %}

<div class='EBI Data Retrieval' markdown='1'>
## **EBI Data Retrieval**
You may retrieve that files necessary to construct a Seurat Object in this way. Doing to will alleviate the necessity to convert AnnData (Python) objects into Seurat (R) objects:
> <hands-on-title>GetData</hands-on-title>
<div class='EBI-Data-Retrieval' markdown='1'>
> <hands-on-title>EBI Data Retrieval</hands-on-title>
>
> You may retrieve that files necessary to construct a Seurat Object in this way. Doing to will alleviate the necessity to convert AnnData (Python) objects into Seurat (R) objects:
>
> Run{% tool [EBI SCXA Data Retrieval](toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2) %} with the following parameters:
> - *"SC-Atlas experiment accession"*: `E-MTAB-6945`
> - *"Choose the type of matrix to download"*: `Raw filtered counts`
{: .hands_on}
</div>
<div class='Importing from a history' markdown='1'>
## **Importing from a history**
You can import [this history](https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data)

{% snippet faqs/galaxy/histories_import.md %}

This also alleviates the necessity to convert the AnnData object into a Seurat one, which is an additional step you must complete if you choose to use the next method.
<div class='Importing-from-a-history' markdown='1'>
> <hands-on-title>Importing from a history</hands-on-title>
> You can import [this history](https://singlecell.usegalaxy.eu/u/camila-goclowski/h/tool-based-seurat-fpe-input-data)
>
> {% snippet faqs/galaxy/histories_import.md %}
>
> This also alleviates the necessity to convert the AnnData object into a Seurat one, which is an additional step you must complete if you choose to use the next method.
{:.hands_on}
</div>
<div class='Uploading from Zenodo' markdown='1'>
## **Uploading from Zenodo**
> <hands-on-title>Option 3: Uploading from Zenodo</hands-on-title>

<div class='Uploading-from-Zenodo' markdown='1'>
> <hands-on-title>Uploading from Zenodo</hands-on-title>
>
> 1. Create a new history for this tutorial
> 2. Import the AnnData object from [Zenodo]({{ page.zenodo_link }})
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