Last updated: 2020-01-11

Checks: 7 0

Knit directory: STUtility_web_site/

This reproducible R Markdown analysis was created with workflowr (version 1.5.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

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Ignored files:
    Ignored:    .Rproj.user/

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Included in STUtility is a Shiny application for manual annotation. It lets the user select and give a/several specific capture-spot(s) a label. This could be used for e.g. visualization or DEA purposes. Instructions for how to use the tool is included in the actual app. By default, the app will open in browser mode. When the annotation is completed, simply close the browser window and return to R.

#NOTE: Following the usual workflow of Seurat, we save the output from the function to our object

se <- ManualAnnotation(se)
 

A work by Joseph Bergenstråhle and Ludvig Larsson

 


sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_Sweden.1252  LC_CTYPE=English_Sweden.1252   
[3] LC_MONETARY=English_Sweden.1252 LC_NUMERIC=C                   
[5] LC_TIME=English_Sweden.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.5.0 Rcpp_1.0.3      rprojroot_1.3-2 digest_0.6.22  
 [5] later_0.8.0     R6_2.4.0        backports_1.1.4 git2r_0.26.1   
 [9] magrittr_1.5    evaluate_0.14   stringi_1.4.3   fs_1.3.1       
[13] promises_1.0.1  rmarkdown_1.15  tools_3.6.1     stringr_1.4.0  
[17] glue_1.3.1      httpuv_1.5.2    xfun_0.9        yaml_2.2.0     
[21] compiler_3.6.1  htmltools_0.3.6 knitr_1.24