.Rbuildignore
.github/.gitignore
.github/workflows/build-checks-devel.yml
.github/workflows/build-checks-release.yml
.github/workflows/docs.yml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R
R/AllGenerics.R
R/CytoImageList-class.R
R/CytoImageList-utils.R
R/CytoImageList.R
R/compImage.R
R/cytomapperShiny.R
R/data.R
R/loadImages.R
R/measureObjects.R
R/namespace.R
R/plotCells.R
R/plotPixels.R
R/plotting-param.R
R/plotting-utils.R
R/server-utils.R
R/shiny-server.R
R/shiny-ui.R
R/subsetting-utils.R
R/validityChecks.R
R/validityChecksShiny.R
README.md
_pkgdown.yml
data/pancreasImages.RData
data/pancreasMasks.RData
data/pancreasSCE.RData
inst/CITATION
inst/extdata/E34_imc.tiff
inst/extdata/E34_mask.tiff
inst/extdata/G01_imc.tiff
inst/extdata/G01_mask.tiff
inst/extdata/J02_imc.tiff
inst/extdata/J02_mask.tiff
inst/scripts/1_LoadPancreasData.Rmd
inst/scripts/2_LoadPancreasImages.Rmd
inst/scripts/3_GenerateToyData.Rmd
inst/scripts/README.md
man/CytoImageList-manipulation.Rd
man/CytoImageList-naming.Rd
man/CytoImageList-subsetting.Rd
man/CytoImageList.Rd
man/compImage.Rd
man/cytomapperShiny.Rd
man/loadImages.Rd
man/measureObjects.Rd
man/pancreasImages.Rd
man/pancreasMasks.Rd
man/pancreasSCE.Rd
man/plotCells.Rd
man/plotPixels.Rd
man/plotting-param.Rd
tests/testthat.R
tests/testthat/_snaps/shiny_ui.md
tests/testthat/_snaps/shiny_ui.new.md
tests/testthat/_snaps/shiny_ui_ondisk.md
tests/testthat/apps/images_app/app.R
tests/testthat/apps/images_app/tests/shinytest.R
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/complex_assay_change.R
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/005.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/005.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/006.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/006.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/007.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/007.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/008.json
tests/testthat/apps/images_app/tests/shinytest/complex_gating-expected/008.png
tests/testthat/apps/images_app/tests/shinytest/complex_gating.R
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/complex_plot_change.R
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/005.json
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tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/006.json
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tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/007.json
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tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/009.json
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change-expected/009.png
tests/testthat/apps/images_app/tests/shinytest/complex_sample_change.R
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/contrasts_set-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/contrasts_set.R
tests/testthat/apps/images_app/tests/shinytest/marker_select-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/marker_select-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/marker_select-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/marker_select-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/marker_select.R
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/005.json
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change-expected/005.png
tests/testthat/apps/images_app/tests/shinytest/simple_assay_change.R
tests/testthat/apps/images_app/tests/shinytest/simple_gating-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/simple_gating-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/simple_gating-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/simple_gating-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/simple_gating.R
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/004.json
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change-expected/004.png
tests/testthat/apps/images_app/tests/shinytest/simple_plot_change.R
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/simple_sample_select.R
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/001.json
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/001.png
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/002.json
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/002.png
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/003.json
tests/testthat/apps/images_app/tests/shinytest/tab_select-expected/003.png
tests/testthat/apps/images_app/tests/shinytest/tab_select.R
tests/testthat/apps/images_app_ondisk/app.R
tests/testthat/apps/images_app_ondisk/tests/shinytest.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/complex_assay_change.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/complex_gating.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/complex_plot_change.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/complex_sample_change.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/contrasts_set.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/marker_select.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/simple_assay_change.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/simple_gating.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/simple_plot_change.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/simple_sample_select.R
tests/testthat/apps/images_app_ondisk/tests/shinytest/tab_select.R
tests/testthat/apps/masks_app/app.R
tests/testthat/apps/masks_app/tests/shinytest.R
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/001.json
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/001.png
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/002.json
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/002.png
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/003.json
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/003.png
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/004.json
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change-expected/004.png
tests/testthat/apps/masks_app/tests/shinytest/complex_assay_change.R
tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/001.json
tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/001.png
tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/002.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/003.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/004.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/005.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/006.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/007.json
tests/testthat/apps/masks_app/tests/shinytest/complex_gating-expected/007.png
tests/testthat/apps/masks_app/tests/shinytest/complex_gating.R
tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/001.json
tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/001.png
tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/002.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/003.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/004.json
tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change-expected/004.png
tests/testthat/apps/masks_app/tests/shinytest/complex_plot_change.R
tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change-expected/001.json
tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change-expected/001.png
tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change-expected/002.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change-expected/003.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change-expected/009.json
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tests/testthat/apps/masks_app/tests/shinytest/complex_sample_change.R
tests/testthat/apps/masks_app/tests/shinytest/marker_select-expected/001.json
tests/testthat/apps/masks_app/tests/shinytest/marker_select-expected/001.png
tests/testthat/apps/masks_app/tests/shinytest/marker_select-expected/002.json
tests/testthat/apps/masks_app/tests/shinytest/marker_select-expected/002.png
tests/testthat/apps/masks_app/tests/shinytest/marker_select.R
tests/testthat/apps/masks_app/tests/shinytest/simple_assay_change-expected/001.json
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tests/testthat/apps/masks_app/tests/shinytest/simple_assay_change.R
tests/testthat/apps/masks_app/tests/shinytest/simple_gating-expected/001.json
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tests/testthat/apps/masks_app/tests/shinytest/simple_gating-expected/002.json
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tests/testthat/apps/masks_app/tests/shinytest/simple_gating.R
tests/testthat/apps/masks_app/tests/shinytest/simple_plot_change-expected/001.json
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tests/testthat/apps/masks_app/tests/shinytest/simple_plot_change.R
tests/testthat/apps/masks_app/tests/shinytest/simple_sample_select-expected/001.json
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tests/testthat/apps/masks_app/tests/shinytest/simple_sample_select.R
tests/testthat/apps/masks_app/tests/shinytest/tab_select-expected/001.json
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tests/testthat/apps/masks_app/tests/shinytest/tab_select-expected/002.json
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tests/testthat/apps/masks_app/tests/shinytest/tab_select.R
tests/testthat/apps/masks_app_ondisk/app.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/complex_assay_change.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/complex_gating.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/complex_plot_change.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/complex_sample_change.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/marker_select.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/simple_assay_change.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/simple_gating.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/simple_plot_change.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/simple_sample_select.R
tests/testthat/apps/masks_app_ondisk/tests/shinytest/tab_select.R
tests/testthat/apps/sce_app/app.R
tests/testthat/apps/sce_app/tests/shinytest.R
tests/testthat/apps/sce_app/tests/shinytest/assay_selection-expected/001.json
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tests/testthat/apps/sce_app/tests/shinytest/assay_selection.R
tests/testthat/apps/sce_app/tests/shinytest/download-expected/001.json
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tests/testthat/apps/sce_app/tests/shinytest/download-expected/002.json
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tests/testthat/apps/sce_app/tests/shinytest/download.R
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tests/testthat/test_CytoImageList-manipulation_ondisk.R
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