navinlabcode / navinlabcode/CellTrek

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Dominant language
R
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Forks
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Description

你好 我在用示例数据进行的时候出现了以下错误
brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors...
Using 2000 features for integration...
Running CCA
Merging objects
Finding neighborhoods
Finding anchors
Found 3730 anchors
Data transfering...
Finding integration vectors
Finding integration vector weights
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Transfering 2000 features onto reference data
Creating new Seurat object...
Warning: Data is of class data.frame. Coercing to dgCMatrix.
Error in CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc, :
no slot of name "counts" for this object of class "Assay5"
In addition: Warning messages:
1: Command ScaleData.RNA changing from SeuratCommand to SeuratCommand
2: Adding image data that isn't associated with any assays

请问是某些R包的版本问题吗

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Research direction

Reproduce the reported CellTrek::traint call with the example data and record the R and package versions. Inspect the path where the new Seurat object is created and the counts slot is accessed. Done means the example runs without the Assay5 counts-slot error or the compatible package versions are documented.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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