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XZouProjects / scCODE

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data
MIT License
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Some doubts about DE_function #1

Closed XUEbaogai0101 closed 2 years ago

XUEbaogai0101 commented 2 years ago

Hi Dr.Zou, I had run an example on scCODE, but I am confused about the 'Detected_times'. I mean, the results were ordered by the 'Detected_times', so the top of the results contained all counts of DE methods, such as 5. But for the next ordered genes of the results, their 'Detected_times' were 4, then how could I know which method was contained in these ordered genes? Thank you very much! XUE

XUEbaogai0101 commented 2 years ago

Besides, forgives my ignorance, could you tell me how to explain the results of 'Z-score-metrics'?

edgeR limma DESeq2 wilcox_test BPSC t_test conquer 0.4944310 1.7003058 -0.2292351 0.2075869 0.6584251 1.6743097 scmap 0.4396737 0.8297328 -5.5151454 -0.9313029 -0.1625449 0.8337633

XZouProjects commented 2 years ago

Hi XUE,

Glad you are interested in our work. Since scCODE would select the appropriate method firstly (default by Top_5), the DE results detected by these methods should be considered reliable. Then, the order by the “Detected times” is made by scCODE as a suggestion. Your concern about the information of the method by which the genes were detected is reasonable. We would provide this information in the coming update, soon.

Best

Xin Zou

发自我的iPhone

在 2022年5月5日，下午5:23，XUEbaogai0101 @.***> 写道：



Besides, forgives my ignorance, could you tell me how to explain the results of 'Z-score-metrics'?

edgeR limma DESeq2 wilcox_test BPSC t_test conquer 0.4944310 1.7003058 -0.2292351 0.2075869 0.6584251 1.6743097 scmap 0.4396737 0.8297328 -5.5151454 -0.9313029 -0.1625449 0.8337633

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XUEbaogai0101 commented 2 years ago

Hi, Dr.Zou! Thanks for your generous answer. I wish you success in your work.

XZouProjects commented 2 years ago

Hi

The algorithm is going to be published on Briefings in bioinformatics. Please refer to the paper.

Thanks

Xin

发自我的iPhone

在 2022年5月6日，下午2:40，XUEbaogai0101 @.***> 写道：



Closed #1https://github.com/XZouProjects/scCODE/issues/1.

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XUEbaogai0101 commented 2 years ago

Yes, of course. I can't wait to see your publication. It's my pleasure to quote your algorithm. Cheer!

XZouProjects commented 2 years ago

This unformated final version, hope it is helpful.

Best

Xin

From: XUEbaogai0101 @.> Sent: Friday, May 6, 2022 11:29 PM To: XZouProjects/scCODE @.> Cc: XZouProjects @.>; Comment @.> Subject: Re: [XZouProjects/scCODE] Some doubts about DE_function (Issue #1)

Yes, of course. I can't wait to see your publishment. It's my pleasure to refer your algorithm. Cheer!

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