Create and use reference without uploading

[GCAT01]

I am working on a small project and have a 10x Visium dataset (mouse brain from one of the vignettes). I used the mouse bulk RNA-seq reference but didn't get many clusters so I wanted to try and create my own. I found this and I think it might be helpful as it is brain specific. However, since this is a small project, I do not want to spend time rigorously verifying expression and cell annotations to upload to celldex. Is there a way I could use the linked dataset as a reference without having to upload it?

[j-andrews7]

Sure. The SingleR documentation covers what goes into the reference object. Pretty much just needs a matrix of counts and the annotations you want to use. That dataset is enormous, so downsampling or creating pseudobulks is probably worthwhile. The SingleR book covers this extensively.

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On Sat, Feb 15, 2025, 4:11 PM GCAT01 ***@***.***> wrote: I am working on a small project and have a 10x Visium dataset (mouse brain from one of the vignettes). I used the mouse bulk RNA-seq reference but didn't get many clusters so I wanted to try and create my own. I found this <https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x> and I think it might be helpful as it is brain specific. However, since this is a small project, I do not want to spend time rigorously verifying expression and cell annotations to upload to celldex. Is there a way I could use the linked dataset as a reference without having to upload it? — Reply to this email directly, view it on GitHub <#33>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACOAQNDDJUKIAFG4LJIJNM32P7CRZAVCNFSM6AAAAABXG5OGWSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2TKNZWGM2DSNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [image: GCAT01]*GCAT01* created an issue (SingleR-inc/celldex#33) <#33> I am working on a small project and have a 10x Visium dataset (mouse brain from one of the vignettes). I used the mouse bulk RNA-seq reference but didn't get many clusters so I wanted to try and create my own. I found this <https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x> and I think it might be helpful as it is brain specific. However, since this is a small project, I do not want to spend time rigorously verifying expression and cell annotations to upload to celldex. Is there a way I could use the linked dataset as a reference without having to upload it? — Reply to this email directly, view it on GitHub <#33>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACOAQNDDJUKIAFG4LJIJNM32P7CRZAVCNFSM6AAAAABXG5OGWSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2TKNZWGM2DSNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>