Comments (4)
Oh, I selected genes from the snRNA variable genes only, which is recommended.
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Wow! that is definitely a good point! Thanks for the message. I will tell the 'quantile_norm' to use my snRNA data as reference.
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I've had Josh's recommendation addressed in a way that reference will be automatically chosen from an RNA dataset if the modalities is properly set when creating a liger object, and a warning will be issued when the reference chosen is of other modalities. This is now available in master branch and will be on CRAN hopefully next week.
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Related Issues (20)
- "shared factor neighborhood" not used anymore as described in the paper? HOT 3
- log transform data first? HOT 1
- Another request for help regarding SCTransform HOT 1
- Generate gene and promoter bed files
- Problems with scaleNotCenter() HOT 2
- Prepare for upcoming Seurat v5 release HOT 1
- Bug in Seurat's wrapper function HOT 1
- cran package archived HOT 6
- NaNs during `SelectGenes()` HOT 1
- Error on makeFeatureMatrix HOT 1
- Dataset specificity plot
- Issue with loading old liger object via convertOldLiger function HOT 3
- Error in `signal_stage()` HOT 4
- invalid type "list" in R_matrix_as_sparse error HOT 3
- no slot name "defaultCluster" for this object of class "liger" HOT 1
- Query on building shared factor neighborhood graph HOT 2
- Error when performing the Wilcoxon test on the peak counts HOT 1
- Error in ImputeKNN
- How can I determine the similarity scores between clusters using Liger's UINMF? HOT 5
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