Last updated: 2021-05-05

Checks: 7 0

Knit directory: STUtility_web_site/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


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The results in this page were generated with repository version 011f70a. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/manual_annotation.png
    Ignored:    pre_data/

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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 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] STutility_0.1.0 ggplot2_3.3.3   Seurat_3.1.5    workflowr_1.6.2

loaded via a namespace (and not attached):
  [1] uuid_0.1-4              backports_1.1.6         systemfonts_0.2.1      
  [4] plyr_1.8.6              igraph_1.2.6            lazyeval_0.2.2         
  [7] sp_1.4-1                splines_4.0.5           crosstalk_1.1.1        
 [10] listenv_0.8.0           digest_0.6.27           foreach_1.5.0          
 [13] htmltools_0.5.1.1       viridis_0.5.1           magick_2.3             
 [16] tiff_0.1-5              gdata_2.18.0            fansi_0.4.2            
 [19] magrittr_2.0.1          cluster_2.1.1           doParallel_1.0.15      
 [22] ROCR_1.0-11             globals_0.14.0          gmodels_2.18.1         
 [25] jpeg_0.1-8.1            colorspace_2.0-0        blob_1.2.1             
 [28] ggrepel_0.9.1           xfun_0.13               dplyr_1.0.5            
 [31] crayon_1.4.1            jsonlite_1.7.2          zeallot_0.1.0          
 [34] survival_3.2-10         zoo_1.8-9               iterators_1.0.12       
 [37] ape_5.4-1               glue_1.4.2              gtable_0.3.0           
 [40] webshot_0.5.2           leiden_0.3.7            future.apply_1.7.0     
 [43] scales_1.1.1            DBI_1.1.0               miniUI_0.1.1.1         
 [46] Rcpp_1.0.6              viridisLite_0.3.0       xtable_1.8-4           
 [49] spData_0.3.5            units_0.6-6             reticulate_1.18        
 [52] spdep_1.1-3             rsvd_1.0.3              akima_0.6-2            
 [55] tsne_0.1-3              htmlwidgets_1.5.3       httr_1.4.2             
 [58] RColorBrewer_1.1-2      ellipsis_0.3.1          ica_1.0-2              
 [61] pkgconfig_2.0.3         uwot_0.1.10             deldir_0.1-25          
 [64] utf8_1.2.1              tidyselect_1.1.0        rlang_0.4.10           
 [67] manipulateWidget_0.10.1 reshape2_1.4.4          later_1.1.0.1          
 [70] munsell_0.5.0           tools_4.0.5             dbscan_1.1-5           
 [73] generics_0.1.0          ggridges_0.5.3          evaluate_0.14          
 [76] stringr_1.4.0           fastmap_1.0.1           yaml_2.2.1             
 [79] knitr_1.28              fs_1.5.0                fitdistrplus_1.1-3     
 [82] rgl_0.100.54            purrr_0.3.4             RANN_2.6.1             
 [85] readbitmap_0.1.5        pbapply_1.4-3           future_1.21.0          
 [88] nlme_3.1-152            mime_0.10               ggiraph_0.7.7          
 [91] compiler_4.0.5          plotly_4.9.3            png_0.1-7              
 [94] e1071_1.7-3             Morpho_2.8              tibble_3.1.0           
 [97] stringi_1.5.3           gdtools_0.2.2           lattice_0.20-41        
[100] Matrix_1.3-2            classInt_0.4-3          shinyjs_1.1            
[103] vctrs_0.3.7             pillar_1.5.1            LearnBayes_2.15.1      
[106] lifecycle_1.0.0         lmtest_0.9-38           RcppAnnoy_0.0.18       
[109] data.table_1.14.0       cowplot_1.1.1           irlba_2.3.3            
[112] Rvcg_0.19.1             raster_3.1-5            httpuv_1.5.2           
[115] patchwork_1.1.1         colorRamps_2.3          R6_2.5.0               
[118] imager_0.42.1           promises_1.2.0.1        KernSmooth_2.23-18     
[121] gridExtra_2.3           bmp_0.3                 parallelly_1.24.0      
[124] codetools_0.2-18        gtools_3.8.2            boot_1.3-27            
[127] MASS_7.3-53.1           assertthat_0.2.1        rprojroot_1.3-2        
[130] withr_2.4.1             sctransform_0.2.1       expm_0.999-4           
[133] parallel_4.0.5          grid_4.0.5              tidyr_1.1.3            
[136] coda_0.19-3             class_7.3-18            rmarkdown_2.1          
[139] Rtsne_0.15              git2r_0.27.1            sf_0.9-7               
[142] shiny_1.4.0.2