Files in akoyabio/phenoptrReports
Create reports using Phenoptics data

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

.lintr

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/analysis_app.R R/component_level_helpers.R R/component_levels_addin.R R/compute_density.R R/consolidate_gadget_addin.R R/count_phenotypes.R R/distance_helpers.R R/excel_helpers.R R/formatters.R R/mean_expression.R R/mean_of_top_and_bottom_cells.R R/mean_of_top_and_bottom_cells_addin.R R/merge_cell_seg_files.R R/merge_gadget_addin.R R/positivity.R R/reports.R R/spatial_map_viewer_addin.R R/spatial_maps.R R/split_phenotypes.R R/staining_consistency_report_addin.R R/unmixing_error_helpers.R R/unmixing_quality_addin.R R/upset_plot.R R/utilities.R README.md

_pkgdown.yml

docs/404.html

docs/LICENSE-text.html

docs/articles/analysis.html

docs/articles/analysis_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/analysis_files/header-attrs-2.3/header-attrs.js

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docs/articles/component_levels_report.html

docs/articles/component_levels_report_files/header-attrs-2.9/header-attrs.js

docs/articles/consolidation.html

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docs/articles/top_20_bottom_10_report.html

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docs/articles/unmixing_error.html

docs/articles/unmixing_quality_report.html

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docs/reference/addin_10_merge.html

docs/reference/addin_20_consolidate.html

docs/reference/addin_30_analysis_app.html

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docs/reference/addin_40_unmixing_quality.html

docs/reference/addin_50_component_levels.html

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docs/reference/addin_70_staining_consistency_report.html

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docs/reference/choose_files.html

docs/reference/component_levels_report.html

docs/reference/compute_density_from_cell_summary.html

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docs/reference/consolidate_and_split_cell_seg_data.html

docs/reference/consolidate_and_summarize_cell_seg_data.html

docs/reference/count_phenotypes.html

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docs/reference/counts_to_percents.html

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docs/reference/staining_consistency_report.html

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docs/reference/upset_plot.html

docs/reference/validate_phenotype_definitions.html

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docs/reference/write_expression_sheet.html

docs/reference/write_h_score_sheet.html

docs/reference/write_mean_of_top_and_bottom_charts.html

docs/reference/write_nearest_neighbor_summary_sheet.html

docs/reference/write_percents_sheet.html

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docs/reference/write_session_info.html

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docs/reference/write_summary_charts.html

docs/reference/write_summary_report.html

docs/reference/write_summary_sheet.html

docs/sitemap.xml

inst/WORDLIST

inst/analysis_app/.gitignore

inst/analysis_app/files_module.R inst/analysis_app/global.R inst/analysis_app/phenotype_module.R inst/analysis_app/server.R inst/analysis_app/ui.R

inst/analysis_app/www/analysis_app.css

inst/etc/AKOYA-Bio-R-Logo-Standard-White.png

inst/rmd/.gitignore

inst/rmd/Akoya.png

inst/rmd/Cell_seg_summary_report.Rmd inst/rmd/Chart_report.Rmd

inst/rmd/Chart_report_template.docx

inst/rmd/Component_levels_report.Rmd inst/rmd/Mean_of_top_and_bottom_charts.Rmd inst/rmd/Staining_consistency_report.Rmd inst/rmd/Unmixing_quality_report.Rmd

inst/rstudio/addins.dcf

inst/spatial_map_viewer_app/global.R inst/spatial_map_viewer_app/phenotype_color_module.R inst/spatial_map_viewer_app/server.R inst/spatial_map_viewer_app/ui.R man/addin_10_merge.Rd man/addin_20_consolidate.Rd man/addin_30_analysis_app.Rd man/addin_35_spatial_map_viewer.Rd man/addin_40_unmixing_quality.Rd man/addin_50_component_levels.Rd man/addin_60_mean_of_top_and_bottom_cells.Rd man/addin_70_staining_consistency_report.Rd man/choose_directory.Rd man/choose_files.Rd man/component_levels_report.Rd man/compute_density_from_cell_summary.Rd man/compute_density_from_table.Rd man/compute_h_score.Rd man/compute_h_score_from_score_data.Rd man/compute_mean_expression.Rd man/compute_mean_expression_many.Rd man/compute_positivity.Rd man/compute_positivity_many.Rd man/consolidate_and_summarize_cell_seg_data.Rd man/count_phenotypes.Rd man/count_within_summary.Rd man/counts_to_percents.Rd man/discrete_colors.Rd

man/figures/Akoya.png

phenoptrReports.Rproj

tests/testthat.R

tests/testthat/_snaps/spatial_maps/from-to-dot-1-no-logo-plot-matches.svg

tests/testthat/_snaps/spatial_maps/from-to-plot-matches.svg

tests/testthat/_snaps/spatial_maps/mutual-plot-matches.svg

tests/testthat/_snaps/spatial_maps/none-plot-matches.svg

tests/testthat/_snaps/spatial_maps/to-from-plot-matches.svg

tests/testthat/test_data/20210728_Top20_Bottom10_Data.docx

tests/testthat/test_data/20210728_Top20_Bottom10_Data.xlsx

tests/testthat/test_data/Consolidated_data.txt

tests/testthat/test_data/FIHC4_Top20_Bottom10.xlsx

tests/testthat/test_data/FIHC4_merge_cell_seg_data.txt

tests/testthat/test_data/Merge2_score_data.txt

tests/testthat/test_data/Merge_cell_seg_data.txt

tests/testthat/test_data/Merge_cell_seg_data_summary.txt

tests/testthat/test_data/Merge_score_data.txt

tests/testthat/test_data/Results.xlsx

tests/testthat/test_data/Results_by_sample.xlsx

tests/testthat/test_data/Top20_Bottom10_Data.xlsx

tests/testthat/test_data/mfg_config.txt

tests/testthat/test_expression.R tests/testthat/test_mean_of_top_and_bottom_cells.R tests/testthat/test_smoke.R tests/testthat/test_spatial_maps.R tests/testthat/test_split_phenotypes.R tests/testthat/test_staining_consistency_report.R tests/testthat/test_utilities.R tools/MakeTestData.R

tools/lintr notes.txt

tools/phenoptr[Reports] issues.txt

tools/test_helpers.R

vignettes/.gitignore

vignettes/analysis.Rmd vignettes/component_levels_report.Rmd vignettes/consolidation.Rmd

vignettes/figures/Analysis_files.png

vignettes/figures/Analyze_addin.png

vignettes/figures/Component_levels_addin.png

vignettes/figures/Component_levels_browse.png

vignettes/figures/Component_levels_create.png

vignettes/figures/Component_levels_options.png

vignettes/figures/Component_levels_options2.png

vignettes/figures/Consolidate_addin.png

vignettes/figures/Create_report.png

vignettes/figures/Create_unmixing_quality_report.png

vignettes/figures/Nearest_neighbor_viewer_main.png

vignettes/figures/Phenotypes.png

vignettes/figures/Phenotypes_with_score.png

vignettes/figures/Process_files.png

vignettes/figures/Processing_please_wait.png

vignettes/figures/Select_export_directory.png

vignettes/figures/Select_merge_files.png

vignettes/figures/Select_output_directory.png

vignettes/figures/Slide_id_prefix.png

vignettes/figures/Spatial_map_viewer_startup.png

vignettes/figures/Spatial_options.png

vignettes/figures/Staining_consistency_addin.png

vignettes/figures/Staining_consistency_bad.png

vignettes/figures/Staining_consistency_browse.png

vignettes/figures/Staining_consistency_create_report.png

vignettes/figures/Staining_consistency_good.png

vignettes/figures/Staining_consistency_select_marker.png

vignettes/figures/Tissue_categories.png

vignettes/figures/Top_20_bottom_10_addin.png

vignettes/figures/Top_20_bottom_10_browse_config.png

vignettes/figures/Top_20_bottom_10_browse_merge.png

vignettes/figures/Top_20_bottom_10_create_report.png

vignettes/figures/Top_20_bottom_10_max_ratio.png

vignettes/figures/Top_20_bottom_10_summarize_by.png

vignettes/figures/Top_20_bottom_10_tissue_categories.png

vignettes/figures/Unmixing_quality_addin.png

vignettes/spatial_map_viewer.Rmd vignettes/staining_consistency_report.Rmd vignettes/top_20_bottom_10_report.Rmd vignettes/unmixing_quality_report.Rmd

akoyabio/phenoptrReports documentation built on Jan. 17, 2022, 6:22 p.m.

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akoyabio/phenoptrReports
Create reports using Phenoptics data

Files in akoyabio/phenoptrReports
Create reports using Phenoptics data

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akoyabio/phenoptrReports Create reports using Phenoptics data

Files in akoyabio/phenoptrReports Create reports using Phenoptics data

R Package Documentation

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akoyabio/phenoptrReports
Create reports using Phenoptics data

Files in akoyabio/phenoptrReports
Create reports using Phenoptics data