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It seems like this issue has popped up a few times with #3557 and #2549. I updated Seurat and Bioconductor to the latest version. I have ~30 different libraries and want to demultiplex all of them. Pr…
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Hi Marc,
Thanks so much for making this code!
I've been running into an issue with SPOTlight version 0.1.7 with my own samples after running the NMF model training and deconvoluting the spots 1…
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Hi,
I used IntegrateData function and obtained error:
Finding integration vector weights
Error in Embeddings(reduction)[nn.cells2, dims] : subscript out of bounds
My anchorset,GABAobj.anch…
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I'm attempting to merge multiple Seurat objects, but I'm getting a class/type-related error. When I attempt to merge them all using `s_merge
I've terminated and started new R sessions, but the iss…
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While merging multiple Seurat objects of multiple modalities (GEX, ATAC and protein), how are chromatin assays merged?
I have read these issues https://github.com/satijalab/seurat/issues/2757 and h…
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Dear colleagues,
I would like to reopen an old issue from January (#3916). Back then, @jgamache014 asked how to obtain all features from datasets in an integrated SCTransformed object for DE analys…
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Dear Seurat team,
I have transcriptome data together with surface protein data (ABSEQ) of PBMCs and I run the multimodel data analysis and WNN, I could also run reference mapping before, but suddenly…
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I got the exact same error as #170 when running sctransform v2 on some Seurat objects. I don't know if it might be connected to size of counts in the file object because it seems to only happen for da…
ceesu updated
11 months ago
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Hi Jack,
SCPA is a great tool for pathway analysis for my Seurat_Objects.
While I can query the Hallmark pathways in the mouse with...
pathways %
format_pathways()
Just need some clarifica…
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Hello,
I have 12 multiome Seurat objects that I want to merge into one. I followed the merging object tutorial here: https://stuartlab.org/signac/articles/merging.html#creating-a-common-peak-set .…