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Hello,
For Xenium 5k , there are two tissue sections in one capture area . I need to analyze every tissue section separately with Seurat.
So could you please tell me how spli…
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**Is your feature request related to a problem? Please describe.**
For the moment, the user has to manually install Seurat in its environments. Or use only conda for checkatlas install.
**Describe…
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Hello,
Thank you for this helpful software!
I have some visium data with biological replicates across several sequencing slides, what is the best way to make use of all data in a co-expression an…
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Hi @evanbiederstedt ,
Is there an equivalent function to this in Seurat https://github.com/satijalab/seurat/issues/3116#issuecomment-640440296 within conos.
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we should provide demo data - not sure how small a dataset makes sense. Possibly 100 cells, where one TCR is tumor reactive? This should be
1. Small to download (download should be possible so th…
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**Description:**
The current implementation of the `CreateNicheDEObjectFromSeurat` lacks support for converting the Seurat 10X Xenium object to the niche-DE format. As a result, users are unable to…
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> netVisual_circle(cellchat_PD@net$weight, vertex.weight = groupSize, weight.scale = T, label.edge= F, title.name = "Interaction weights/strength in PD",arrow.size = 0.05)
Error in i_set_vertex_attr(…
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Hi,
Thank you for developing this incredibly useful pipeline. It has been instrumental in my scRNA-seq analysis work. I have encountered an interesting issue while using the script provided: when u…
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### Description of feature
Dear all
I just found out that in commit https://github.com/nf-core/scrnaseq/commit/aae5fc5f618d1a4ccd40428d14050d838876f7fe we moved away from having ensembl_gene_ids a…
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Hi Dr. Hou, it's great to have an alternative to try in relation to tradeseq - I thought the paper was clear and an interesting read. I was wondering what expected runtimes may be for the lamian_test …