Making Seurat tools usable for researchers

[nomadscientist]

Some tools currently in Scanpy need Seurat versions to make Seurat tools usable for researchers, which would be helpful given that stuff like Monocl/cell annotation/etc. are more available with R objects and python ones.

• Plot with Seurat
• Plot embed
• Inspect Seurat object
• Seurat Object Operations
• Manipulate Seurat object

[pcm32]

Good stuff, thanks! Have you seen if any of that functionality is covered by this tool: https://singlecell.usegalaxy.eu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseurat%2Fseurat%2F3.2.2%2Bgalaxy0 ?

[nomadscientist]

That tool is an all-in-one, which is great, but if I wanted to do more in-depth stuff using individual tools, or play around with things or move them between scanpy/seurat, etc., I'd need the other singular tools.

…

On Mon, Apr 26, 2021 at 3:15 PM Pablo Moreno ***@***.***> wrote: Good stuff, thanks! Have you seen if any of that functionality is covered by this tool: https://singlecell.usegalaxy.eu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseurat%2Fseurat%2F3.2.2%2Bgalaxy0 ? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#222 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKUKCSPVP35BAKVOSSD6SQTTKVYP7ANCNFSM4ZMHTSXA> .

[nomadscientist]

@Camila-goclowski

[nomadscientist]

@pcm32 Hello! I have a lovely intern, Camila, who is going to make a tutorial with the Seurat tools to mirror the Scanpy one. Is it possible to get the above tool requests sorted on your team's end?

[nomadscientist]

@pcm32 - This tool that you mention - https://singlecell.usegalaxy.eu/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseurat%2Fseurat%2F3.2.2%2Bgalaxy0 - does not allow inclusion of metadata (like genotype, disease, etc.). This makes it quite hard to use for analysis / plotting...

[pcm32]

Hi, apologies for the long delay. Unfortunately we have been short of hands at the team for most of last year or so. We had a new team member arriving to help in August and we expect a another member to start soon (for people who left in March and July or so). So it would be hard for me to make any promises here :-(.