Quang Nguyen

Error: How to solve the fact that goplot keeps asking for text input?

2

Hi there, I aim to goplot() `ego` output, but it keeps giving me a "?" asking for some text input as below. What is interesting was the ego object `egoGOEnrichGeneSet`...

Hi there, I performed `(A) FindAllMarkers(test.use = "wilcox")`. I then ran using the same Seurat object `(B) FindAllMarkers(now setting assay = "SCT", only.pos = F, recorrect_umi = FALSE, test.use="MAST", latent.vars="donor_ID")`....

Following issues #5761 and #4115, Would you mind letting me know how to get variable feature info if we selected the variable features for a merged Seurat object using `SelectIntegrationFeatures()`?...

Hi there, My dataset when merged showed a high impact in clustering by `donor_ID`. So I want to subtract out this donor effect. Question 1. Would you mind helping me...

Utility of the "new" active.ident: Do we need to change cluster names before merging in computing de novo UMAP?

2

Hi there, I have 2 Seurat objects which were SCTransform-ed (v2) individually and carried through clustering analysis. I now want to compute the de novo UMAP visualization to see which...

Related to #5734, after I performed MapQuery() of my query data onto the ref CITE-seq data (following https://satijalab.org/seurat/articles/multimodal_reference_mapping.html#example-2-mapping-human-bone-marrow-cells-1), I switched to the active assay `prediction.score.celltype.l2` to visualize the prediction scores...

SeuratWrappers Install: How to solve "Error: Failed to install 'unknown package' from GitHub:"?

2

Hi, I tried to install the package, but encountered the error below. Would you mind advising on how to proceed? Thank you! ``` > remotes::install_github('satijalab/seurat-wrappers') Downloading GitHub repo satijalab/seurat-wrappers@HEAD Error:...

Could not find index file but still generated the loom from bam -- run10x error?

8

After so many attempts (solved in #320), I finally generated a loom file from my count output from cellranger 10x. Nevertheless, when I examined the error log, it said "Could...

Hi there, It was advised to re-run SCTransform to get a new vector of variable genes after removing cells from the object. Nevertheless, given that SCTransform is recommended to be...

Related to the bugs in #4018 and #6412, `VariableFeaturePlot()` produced "incorrect number of dimensions" error for merged SCTransform-ed objects. Would you mind advising us how to proceed to obtain the...