User: yuhongruoyi

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yuhongruoyi10
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Posts by yuhongruoyi

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Comment: C: CellCycleScoring in Seurat with custom cell-cycle gene list
... Hello, I also encounterred this Seurat v3.0 CellCycleScoring Error.And I have normalized my data and try it again as you said.But it didn't work. Do you have any other solutions? > cc.genes <- readLines(con = "D:/personal data/cell_cycle_vignette_files/regev_lab_cell_cycle_genes.txt")` ...
written 6 months ago by yuhongruoyi10
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Comment: C: Convert loom file to Seurat
... Thank you, the convert function is defunct.Now we can just convert seurat to loom,not in reverse. So we can only wait,no other solutions? ...
written 6 months ago by yuhongruoyi10
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Comment: C: Convert loom file to Seurat
... How do you know that converting to and from loom files is currently unavailable?Did you ask the seurat team? ...
written 6 months ago by yuhongruoyi10
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Comment: C: Convert loom file to Seurat
... yes, I also use Seurat v3.I see that:[seurat offers a conversion function to go from Seurat objects to loom files. The reverse conversion is currently in progress.][1].Do you know that when they will restore this functionality? I need to merge my seurat data with the data provided by loom edition(ht ...
written 6 months ago by yuhongruoyi10
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Comment: A: Convert loom file to Seurat
... have you found the solution? ...
written 6 months ago by yuhongruoyi10
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How to use monocle to import a loom file?
... I want to merge my seurat data of 3 experimental time points with the Hippocampus data provided by loom edition. .But I don't know how to convert this loom file to expression matrix or other CDS that monocle can recognize. I know monocle can import seurat object, but the seurat tutorial says that : ...
R monocle rna-seq seurat written 6 months ago by yuhongruoyi10 • updated 5 weeks ago by Biostar ♦♦ 20
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Delete custom additional column from Seurat metadata
... I add some columns of custom metadata by using the Seurat v3.X command `object$name <- vector`, but I can't delete these columns, such as `"time"`, `"hours"`. I try many many ways, like subset, subsetdata, and `test.tc11$hours <- NULL`, all them didn't work. Can you help me? > test.tc ...
R rna-seq seurat written 6 months ago by yuhongruoyi10 • updated 6 months ago by Friederike5.1k
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Seurat object can't be imported into monocle:the object type you want to export to is not supported yet
... Hello, I was wondering why my Seurat object can't be imported into monocle? I follow the official website to do it, but it turns out that the importCDS doesn't take that. Below is the R code and my sessioninfo: If you do know of how to might help us, that would be incredibly helpful! Thank ...
R monocle seurat single cell rna-seq written 7 months ago by yuhongruoyi10 • updated 6 months ago by lina.kroehling20
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R failed to configure hdf5 working with loom files in Seurat
... Working with loom files in Seurat, I need to setup the loom Object and get the HDF5 C++ API following [this link][5]. My hdf5-1.8.14.zip file was obtained from [this link][4] , then unpacked to `C:\hdf5`, and I used the version of `cmake-3.13.4-win64-x64` and visual studio 2017 to configure, but it ...
software error R rna-seq written 7 months ago by yuhongruoyi10 • updated 7 months ago by RamRS24k

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