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