User: Xingyu

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Xingyu0
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Posts by Xingyu

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Cannot install AUCell 1.2.2
... Thanks very much! ...
written 17 months ago by Xingyu0
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Cannot install AUCell 1.2.2
... Hi, I noticed that SCENIC has been updated two days ago and uses AUCell 1.2.2 or higher now. But I cannot find 1.2.2 in Bioconductor and the link provided by the tutorial (install.packages("https://bioconductor.org/packages/release/bioc/src/contrib/AUCell_1.2.2.tar.gz", repos=NULL) cannot work. Is ...
aucell scenic written 17 months ago by Xingyu0 • updated 17 months ago by sara.aibar10
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The explanation of plotExplanatoryVariables plot
... Hi, I'm learning this workflow of single cell analysis and I'm very confused about the explanation of the plot of plotExplanatoryVariables function. In the section 2.7, you mentioned that "The percentages are generally small (1-3%), indicating that the expression profiles of most genes are not stro ...
simplesinglecell written 20 months ago by Xingyu0 • updated 20 months ago by Aaron Lun25k
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Comment: C: The selection of bandwidth of GSVA
... Thanks very much. I'm now trying to tune the Sigma parameter '4' in the GSVA package. I directly changed this parameter in the src C code of GSVA source package. Hope that will work. ...
written 20 months ago by Xingyu0
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Comment: C: The selection of bandwidth of GSVA
... Hi Robert, I wonder is there a quantitative metric for evaluating how well it worked or just chose one which gave best results? Thanks so much! Xingyu ...
written 20 months ago by Xingyu0
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The selection of bandwidth of GSVA
... Hi, I'm learning GSVA paper recently and I'm wondering why GSVA chose Si/4 as the bandwidth for a Gaussian kenel estimation. I have read all the document I can find for GSVA but still didn't find the answer. Could you please give me the reason of this choice? Thanks! ...
gsva written 20 months ago by Xingyu0 • updated 20 months ago by Robert Castelo2.3k
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Comment: C: SingleCellExperiment object cannot be used by Scater package?
... Hi Aaron, Thanks for your answer. Yes, I checked it and found it was an old version because I used the old version of Bioconductor. After I updated it and reinstall the latest version of scater, it works well! Thanks so much!   ...
written 21 months ago by Xingyu0
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SingleCellExperiment object cannot be used by Scater package?
... Hi, I'm learning how to do simple analysis to single cell sequencing data from this workflow http://bioconductor.org/help/workflows/simpleSingleCell/#denoising-expression-values-using-pca#cmid=172561 In the QC step, it used the function calculateQCMetrics. But I got warning: Error in calculateQCMe ...
scater simplesinglecell singlecellexperiment written 21 months ago by Xingyu0 • updated 21 months ago by Aaron Lun25k

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