Longda

Hi @denvercal1234GitHub , Re Q1 and Q2: By generating the de novo UMAP after merging 2 datasets, we are able to look for cell clusters that are not shared by...

Hi @denvercal1234GitHub, Sorry for the late reply! Re 1). Yes you are right. de novo UMAP is always worth looking into due to the potential existence of these dataset-specific cell...

Hi @paulstumpges , This is a strange behavior. If you set the split.plot = F are you able to get a normal shape for your mutant group? Or is it...

Hi @rbutleriii, You may try running AverageExpression() first to filter the genes. For example: ``` ave_exp = AverageExpression(object = sc, assays = "RNA", features = tasic_cort) ``` You can remove...

Hi, Could you please let me know what is each column representing? Is each column here representing a single cell or a pseudo-bulked cell type/cluster? In addition, how is DEG...

Hi, Did you run SCTransform when you are generating these objects? It seems that SCTAssay is causing the problem. In addition, what other commands did you run before merging (you...

Hi, I see. Thank you for the information. Can you quickly check the `str([email protected])` and `str([email protected])`? Just to make sure the SCTModel.list object exists in both of your Seurat.objects. Also,...

Hi, Thank you for noticing this issue. Although this is not a bug (as mentioned in https://github.com/satijalab/seurat/issues/6110#issuecomment-1172650788), this auto-flip will indeed distort the x and y ratio. We will likely...

Hi, I am closing this issue for now as we have not got any response. Will reopen it if there is any update.

Hi, This bug does not seem to exist for the latest version of Seurat. I am closing this issue now but feel free to re-open it if the issue persists.