Applying of Seurat cell-clustering analysis in SingleR

[erikfel97]

Hi All! I'm currently working on my first project of Single Cell analysis and it will be great to have your advice. I did all the necessary analysis of mt data with Surat - including combining 5 data sets, filtering the cells, normalizing and scaling the expression values, etc. I finally cluster the pre-processed data and found 25 cell clusters, now I need to annotate them. As I understand from the vignette, I should provide SingleR with the counts. Two questions: 1, Is there any option to use the differential expressed marker gene output of Seurat to insure that SingleR analysis will define the same 25 clusters?

2. Which pre-processing is required for the input data?

Best, Erik

[dviraran]

Please repost these questions in https://github.com/LTLA/SingleR.

Best, Dvir

[erikfel97]

Hi Dvir, Thank you very much for your fast response. If you don't mind I have one more question, I tried to install the SingleR package using this code: devtools::install_github('dviraran/SingleR')

But all the time I receive the same error massage: Installing package into ‘C:/Users/ShenorrLab/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) ERROR: failed to lock directory 'C:/Users/ShenorrLab/Documents/R/win-library/3.6' for modifying Try removing 'C:/Users/ShenorrLab/Documents/R/win-library/3.6/00LOCK-SingleR' Error: Failed to install 'SingleR' from GitHub: (converted from warning) installation of package ‘C:/Users/SHENOR~1/AppData/Local/Temp/RtmpyImYao/fileaf470051d00/SingleR_1.0.1.tar.gz’ had non-zero exit status

Do you have any suggestions?

Best Regards, Erik

---

מאת: dviraran notifications@github.com ‏‏נשלח: יום שישי 01 נובמבר 2019 00:31 ‏‏אל: dviraran/SingleR SingleR@noreply.github.com עותק: Erik Feldman erik.feldman@campus.technion.ac.il; Author author@noreply.github.com ‏‏נושא: Re: [dviraran/SingleR] Applying of Seurat cell-clustering analysis in SingleR (#120)

Please repost these questions in https://github.com/LTLA/SingleRhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FLTLA%2FSingleR&data=02%7C01%7Cerik.feldman%40campus.technion.ac.il%7C37cf6ea7aada4fa1536c08d75e520cfd%7Cf1502c4cee2e411c9715c855f6753b84%7C1%7C0%7C637081578869608869&sdata=02WiqskVlhwQg6A2VLebShxTymdNMfDRve%2BKwAx1Kuc%3D&reserved=0.

Best, Dvir

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[erikfel97]

Problem solved by deleting the "locked" folder in the packages installation directory and re-installing SingleR