solvi808

Results 9 comments of solvi808

Seurat FindClusters() Error when running addDoubletScores() and addIterativeLSI() ----> no slot of name "i" for this object of class "Graph"

Hello, sure. **Here is the traceback from addDoubletScores()** ``` 12: stop("Exiting See Error Above") 11: .logError(e, fn = "addIterativeLSI", info = prefix, errorList = list(ArrowFile = ArrowFile), logFile = logFile)...

Seurat FindClusters() Error when running addDoubletScores() and addIterativeLSI() ----> no slot of name "i" for this object of class "Graph"

Hello, I have not but perhaps now with a different Seurat release it will be fixed (one can hope) Since a reproducible example is needed, I could perhaps upload the...

Option to change the image resolution in ggplot_image() ?

I have made a quick suggestion/solution to fix this at https://github.com/rstudio/gt/pull/1485

run_umap errors [BUG]

Reporting the same error: I am running the latest version of SCENIC+ with python3.11 . 2024-08-22 20:47:19,339 cisTopic INFO Running UMAP ``` Traceback (most recent call last): File "/home/ulb/iribhm/gwindels/WORKSITE1/phase_2_combined_integration_ONE/SPLUS//LOGS//pycisTopic_run_part3//PIPELINE_MAINSKRIPT.py", line...

export_pseudobulk error

I got the same error, and it said the package pyrle was missing, so after installing pyrle the output files appeared. Perhaps it is not correctly defined in the dependencies?

Another error with addIterativeLSI - "Error in clusterDF$clusters : $ operator is invalid for atomic vectors"

UPDATE: The error seems to go away when I set the option of clusterParams with resolution = 0.2 instead of the 2 defaults. this gives the original error: ``` proj

Error whilst subsetting a Seurat 5 object: Error in check_valid_matrix(x) : no slot of name "i" for this object of class "Graph"

Also getting this issue persistently after subsetting a seurat object. When will this be fixed ? ``` > moSCO

Plots showing projection of perturbation effect in embedding look the same for all regulons

Hello, Ok I did as you suggested but I cannot see any co-expression between the TFs that explains the similarity between the perturbation-velocity plots I also attached the jupyter notebook...

Ability to add dividers between plots?

Seconding that this would be useful, f.ex. me I want to make 3 column x 20 row item plots, but split it into two page-columns so that I have 2...