Last updated: 2020-06-03

Checks: 6 1

Knit directory: STUtility_web_site/

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File Version Author Date Message
html fb06450 jbergenstrahle 2020-01-11 Build site.
Rmd baff98e jbergenstrahle 2019-12-16 adding
Rmd 5cb8ab1 jbergenstrahle 2019-12-02 update2

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 4.0.0 (2020-04-24)
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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] STutility_0.1.0             ggplot2_3.3.0              
 [3] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.1
 [5] DelayedArray_0.14.0         matrixStats_0.56.0         
 [7] Biobase_2.48.0              GenomicRanges_1.40.0       
 [9] GenomeInfoDb_1.24.0         IRanges_2.22.1             
[11] S4Vectors_0.26.0            BiocGenerics_0.34.0        
[13] Seurat_3.1.5               

loaded via a namespace (and not attached):
  [1] reticulate_1.15         tidyselect_1.0.0        htmlwidgets_1.5.1      
  [4] grid_4.0.0              Rtsne_0.15              munsell_0.5.0          
  [7] codetools_0.2-16        ica_1.0-2               units_0.6-6            
 [10] future_1.17.0           miniUI_0.1.1.1          withr_2.2.0            
 [13] colorspace_1.4-1        knitr_1.28              uuid_0.1-4             
 [16] ROCR_1.0-11             tensor_1.5              listenv_0.8.0          
 [19] git2r_0.27.1            GenomeInfoDbData_1.2.3  polyclip_1.10-0        
 [22] rprojroot_1.3-2         coda_0.19-3             LearnBayes_2.15.1      
 [25] vctrs_0.3.0             xfun_0.13               R6_2.4.1               
 [28] doParallel_1.0.15       rsvd_1.0.3              Morpho_2.8             
 [31] ggiraph_0.7.0           manipulateWidget_0.10.1 bitops_1.0-6           
 [34] spatstat.utils_1.17-0   assertthat_0.2.1        promises_1.1.0         
 [37] scales_1.1.0            imager_0.42.1           gtable_0.3.0           
 [40] npsurv_0.4-0.1          globals_0.12.5          bmp_0.3                
 [43] goftest_1.2-2           workflowr_1.6.2         rlang_0.4.6            
 [46] zeallot_0.1.0           akima_0.6-2             systemfonts_0.2.1      
 [49] splines_4.0.0           lazyeval_0.2.2          rgl_0.100.54           
 [52] yaml_2.2.1              reshape2_1.4.4          abind_1.4-5            
 [55] crosstalk_1.1.0.1       backports_1.1.6         httpuv_1.5.2           
 [58] tools_4.0.0             spData_0.3.5            ellipsis_0.3.0         
 [61] raster_3.1-5            RColorBrewer_1.1-2      Rvcg_0.19.1            
 [64] ggridges_0.5.2          Rcpp_1.0.4.6            plyr_1.8.6             
 [67] zlibbioc_1.34.0         classInt_0.4-3          purrr_0.3.4            
 [70] RCurl_1.98-1.2          rpart_4.1-15            dbscan_1.1-5           
 [73] deldir_0.1-25           viridis_0.5.1           pbapply_1.4-2          
 [76] cowplot_1.0.0           zoo_1.8-8               ggrepel_0.8.2          
 [79] cluster_2.1.0           colorRamps_2.3          fs_1.4.1               
 [82] magrittr_1.5            data.table_1.12.8       magick_2.3             
 [85] readbitmap_0.1.5        gmodels_2.18.1          lmtest_0.9-37          
 [88] RANN_2.6.1              whisker_0.4             fitdistrplus_1.0-14    
 [91] patchwork_1.0.0         shinyjs_1.1             lsei_1.2-0.1           
 [94] mime_0.9                evaluate_0.14           xtable_1.8-4           
 [97] jpeg_0.1-8.1            gridExtra_2.3           compiler_4.0.0         
[100] tibble_3.0.1            KernSmooth_2.23-17      crayon_1.3.4           
[103] htmltools_0.4.0         mgcv_1.8-31             later_1.0.0            
[106] spdep_1.1-3             tiff_0.1-5              tidyr_1.0.3            
[109] expm_0.999-4            DBI_1.1.0               MASS_7.3-51.6          
[112] sf_0.9-3                boot_1.3-25             Matrix_1.2-18          
[115] gdata_2.18.0            igraph_1.2.5            pkgconfig_2.0.3        
[118] sp_1.4-1                plotly_4.9.2.1          xml2_1.3.2             
[121] foreach_1.5.0           webshot_0.5.2           XVector_0.28.0         
[124] stringr_1.4.0           digest_0.6.25           sctransform_0.2.1      
[127] RcppAnnoy_0.0.16        tsne_0.1-3              spatstat.data_1.4-3    
[130] rmarkdown_2.1           leiden_0.3.3            uwot_0.1.8             
[133] gdtools_0.2.2           gtools_3.8.2            shiny_1.4.0.2          
[136] lifecycle_0.2.0         nlme_3.1-147            jsonlite_1.6.1         
[139] viridisLite_0.3.0       pillar_1.4.4            lattice_0.20-41        
[142] fastmap_1.0.1           httr_1.4.1              survival_3.1-12        
[145] glue_1.4.0              spatstat_1.63-3         png_0.1-7              
[148] iterators_1.0.12        class_7.3-17            stringi_1.4.6          
[151] dplyr_0.8.5             irlba_2.3.3             e1071_1.7-3            
[154] future.apply_1.5.0      ape_5.3