Files in RGLab/flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/workflows/build.yml
.gitignore
.travis.yml
DESCRIPTION
INSTALL
LICENSE
Meta/vignette.rds
NAMESPACE
NEWS.md
R/AllClasses.R
R/GatingHierarchy_Methods.R
R/GatingSetList_Methods.R
R/GatingSet_Methods.R
R/add_Methods.R
R/copyNode.R
R/cpp11.R
R/cytoframe.R
R/cytoset.R
R/deprecated.R
R/filterObject_Methods.R
R/flow_trans.R
R/getDescendants.R
R/getSingleCellExpression.R
R/getStats.R
R/identifier.R
R/load_fcs.R
R/load_gs.R
R/merge_GatingSet.R
R/merge_gslist.R
R/moveNode.R
R/parse_transformer.R
R/setGate_Methods.R
R/updateIndices.R
R/utils.R
R/zzz.R
README.md
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
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docs/apple-touch-icon.png
docs/articles/HowToMergeGatingSet.html
docs/articles/HowToMergeGatingSet_files/accessible-code-block-0.0.1/empty-anchor.js
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docs/articles/HowToMergeGatingSet_files/figure-html/unnamed-chunk-9-2.png
docs/articles/HowToMergeGatingSet_files/header-attrs-2.3/header-attrs.js
docs/articles/flowWorkspace-Introduction.html
docs/articles/flowWorkspace-Introduction_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/flowWorkspace-Introduction_files/figure-html/autoplot-gh-bool-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/autoplot-multiple-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/autoplot-nodeName-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/autoplot-rect-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/gh_plot_pop_count_cv-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/plot-gh-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/plotTree-1.png
docs/articles/flowWorkspace-Introduction_files/figure-html/unnamed-chunk-5-1.png
docs/articles/flowWorkspace-Introduction_files/header-attrs-2.3/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/logo_mid.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/GatingHierarchy-class-1.png
docs/reference/GatingHierarchy-class-2.png
docs/reference/GatingHierarchy-class.html
docs/reference/GatingSet-class.html
docs/reference/GatingSet-methods.html
docs/reference/GatingSetList-class.html
docs/reference/asinh_Gml2.html
docs/reference/asinhtGml2_trans.html
docs/reference/booleanFilter-class.html
docs/reference/brackets.html
docs/reference/cf_append_cols.html
docs/reference/cf_get_h5_file_path.html
docs/reference/cf_write_h5.html
docs/reference/cleanup_temp.html
docs/reference/compensate-cytoframe-matrix-method.html
docs/reference/compensate.html
docs/reference/compute_timestep.html
docs/reference/convert.html
docs/reference/convert_legacy.html
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docs/reference/cs_set_cytoframe.html
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docs/reference/cytoframe-keywords.html
docs/reference/cytoframe-labels.html
docs/reference/cytoframe.html
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docs/reference/estimateLogicle.GatingHierarchy.html
docs/reference/estimateLogicle.html
docs/reference/extract_cluster_pop_name_from_node.html
docs/reference/filterObject.html
docs/reference/filter_to_list.html
docs/reference/fix_channel_slash.html
docs/reference/flowJo_flog.html
docs/reference/flowWorkspace-deprecated.html
docs/reference/flowWorkspace-package.html
docs/reference/flowWorkspace.par.get.html
docs/reference/flowWorkspace.par.init.html
docs/reference/flow_breaks.html
docs/reference/flow_trans.html
docs/reference/flowjo_biexp.html
docs/reference/flowjo_biexp_trans.html
docs/reference/flowjo_fasinh.html
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docs/reference/gh_copy_gate.html
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docs/reference/gh_get_transformations.html
docs/reference/gh_pop_compare_stats.html
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docs/reference/gh_pop_get_data.html
docs/reference/gh_pop_get_descendants.html
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docs/reference/gh_pop_get_gate.html
docs/reference/gh_pop_get_indices.html
docs/reference/gh_pop_get_indices_mat.html
docs/reference/gh_pop_get_proportion.html
docs/reference/gh_pop_move.html
docs/reference/gh_pop_set_indices.html
docs/reference/gh_pop_set_xml_count.html
docs/reference/gs_check_redundant_nodes.html
docs/reference/gs_clone.html
docs/reference/gs_cyto_data.html
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docs/reference/gs_get_singlecell_expression.html
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docs/reference/gs_pop_add.html
docs/reference/gs_pop_get_children.html
docs/reference/gs_pop_get_count_fast.html
docs/reference/gs_pop_get_data.html
docs/reference/gs_pop_get_gate.html
docs/reference/gs_pop_get_stats.html
docs/reference/gs_pop_get_stats_tfilter.html
docs/reference/gs_pop_set_gate.html
docs/reference/gs_pop_set_name.html
docs/reference/gs_pop_set_visibility.html
docs/reference/gs_remove_redundant_channels.html
docs/reference/gs_remove_redundant_nodes.html
docs/reference/gs_split_by_channels.html
docs/reference/gs_split_by_tree.html
docs/reference/gs_update_channels.html
docs/reference/gslist_to_gs.html
docs/reference/identifier-methods.html
docs/reference/index.html
docs/reference/keyword.html
docs/reference/lapply-methods.html
docs/reference/length.html
docs/reference/load_cytoframe_from_fcs.html
docs/reference/load_cytoframe_from_h5.html
docs/reference/load_cytoset_from_fcs.html
docs/reference/load_meta.html
docs/reference/lock.html
docs/reference/logicleGml2_trans.html
docs/reference/logicle_trans.html
docs/reference/loglevel.html
docs/reference/logtGml2_trans.html
docs/reference/markernames.html
docs/reference/merge_list_to_gs.html
docs/reference/ncFlowSet-methods.html
docs/reference/nodeflags.html
docs/reference/openWorkspace.html
docs/reference/pData-methods.html
docs/reference/plot-methods.html
docs/reference/plotGate-methods-defunct.html
docs/reference/pop_add.html
docs/reference/prettyAxis.html
docs/reference/recompute.html
docs/reference/rotate_gate.html
docs/reference/sampleNames-character-method.html
docs/reference/sampleNames.html
docs/reference/save_cytoset.html
docs/reference/save_gs.html
docs/reference/scale_gate.html
docs/reference/shift_gate.html
docs/reference/standardize-GatingSet.html
docs/reference/stats.fun.html
docs/reference/subset.html
docs/reference/swap_data_cols.html
docs/reference/transform.html
docs/reference/transform_gate.html
docs/reference/transformerList.html
inst/extdata/empty_workspace_9.2.xml
inst/include/flowWorkspace.h
inst/include/flowWorkspace/convert_to_str_idx.h
inst/include/flowWorkspace/convert_trans.h
inst/include/flowWorkspace/list_to_comp.h
inst/include/flowWorkspace/pairVectorCpp11Convert.h
inst/javascript/showPlot.js
logo.png
logo_mid.png
man-roxygen/template-depr_fun.R
man-roxygen/template-depr_pkg.R
man/GatingHierarchy-class.Rd
man/GatingSet-class.Rd
man/GatingSet-methods.Rd
man/GatingSetList-class.Rd
man/asinh_Gml2.Rd
man/asinhtGml2_trans.Rd
man/booleanFilter-class.Rd
man/brackets.Rd
man/cf_append_cols.Rd
man/cf_backend_type.Rd
man/cf_get_uri.Rd
man/cf_write_disk.Rd
man/cf_write_h5.Rd
man/cleanup.Rd
man/cleanup_temp.Rd
man/compensate.Rd
man/convert.Rd
man/convert_backend.Rd
man/convert_legacy.Rd
man/cs_add_cytoframe.Rd
man/cs_get_uri.Rd
man/cs_set_cytoframe.Rd
man/cytoframe-labels.Rd
man/cytoframe.Rd
man/cytoset.Rd
man/default_backend.Rd
man/delete_gs.Rd
man/estimateLogicle.Rd
man/extract_cluster_pop_name_from_node.Rd
man/filter_to_list.Rd
man/flowWorkspace-deprecated.Rd
man/flowWorkspace-package.Rd
man/flow_breaks.Rd
man/flow_trans.Rd
man/flowjo_biexp.Rd
man/flowjo_biexp_trans.Rd
man/flowjo_fasinh.Rd
man/flowjo_fasinh_trans.Rd
man/flowjo_log_trans.Rd
man/gh_apply_to_cs.Rd
man/gh_apply_to_new_fcs.Rd
man/gh_copy_gate.Rd
man/gh_get_cluster_labels.Rd
man/gh_get_compensations.Rd
man/gh_get_transformations.Rd
man/gh_pop_compare_stats.Rd
man/gh_pop_get_cluster_name.Rd
man/gh_pop_get_data.Rd
man/gh_pop_get_descendants.Rd
man/gh_pop_get_full_path.Rd
man/gh_pop_get_indices.Rd
man/gh_pop_get_indices_mat.Rd
man/gh_pop_get_proportion.Rd
man/gh_pop_move.Rd
man/gh_pop_set_indices.Rd
man/gh_pop_set_xml_count.Rd
man/gs_check_redundant_nodes.Rd
man/gs_cyto_data.Rd
man/gs_get_compensation_internal.Rd
man/gs_get_leaf_nodes.Rd
man/gs_get_pop_paths.Rd
man/gs_get_singlecell_expression.Rd
man/gs_is_persistent.Rd
man/gs_plot_diff_tree.Rd
man/gs_plot_pop_count_cv.Rd
man/gs_pop_add.Rd
man/gs_pop_get_children.Rd
man/gs_pop_get_count_fast.Rd
man/gs_pop_get_gate.Rd
man/gs_pop_get_gs.Rd
man/gs_pop_get_stats.Rd
man/gs_pop_get_stats_tfilter.Rd
man/gs_pop_set_gate.Rd
man/gs_pop_set_name.Rd
man/gs_pop_set_visibility.Rd
man/gs_remove_redundant_channels.Rd
man/gs_remove_redundant_nodes.Rd
man/gs_split_by_channels.Rd
man/gs_split_by_tree.Rd
man/gs_update_channels.Rd
man/gslist_to_gs.Rd
man/identifier-methods.Rd
man/is_subsetted.Rd
man/keyword-mutators.Rd
man/keyword.Rd
man/lapply-methods.Rd
man/length.Rd
man/load_cytoframe.Rd
man/load_cytoframe_from_fcs.Rd
man/load_cytoset_from_fcs.Rd
man/load_meta.Rd
man/lock.Rd
man/logicleGml2_trans.Rd
man/logicle_trans.Rd
man/loglevel.Rd
man/logtGml2_trans.Rd
man/markernames.Rd
man/merge_list_to_gs.Rd
man/ncFlowSet-methods.Rd
man/nodeflags.Rd
man/openWorkspace.Rd
man/pData-methods.Rd
man/plot-methods.Rd
man/pop_add.Rd
man/prettyAxis.Rd
man/recompute.Rd
man/rotate_gate.Rd
man/sampleNames.Rd
man/save_cytoset.Rd
man/save_gs.Rd
man/scale_gate.Rd
man/shift_gate.Rd
man/standardize-GatingSet.Rd
man/stats.fun.Rd
man/subset.Rd
man/swap_data_cols.Rd
man/transform.Rd
man/transform_gate.Rd
man/transformerList.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/Makevars
src/Makevars.ucrt
src/Makevars.win
src/R_API.cpp
src/R_GatingHierarchy.cpp
src/R_GatingSet.cpp
src/cpp11.cpp
src/cytoframeAPI.cpp
src/cytosetAPI.cpp
src/flowWorkspace_types.h
src/getDescendants.cpp
src/getPopStats.cpp
src/getSingleCellExpression.cpp
src/h5_error_r_handler.cpp
src/setCounts.cpp
tests/testthat.R
tests/testthat/GatingHierarchy-testSuite.R
tests/testthat/GatingSet-testSuite.R
tests/testthat/IO-testSuite.R
tests/testthat/cleanup_temp.R
tests/testthat/comp-trans-gs.R
tests/testthat/convert-legacy.R
tests/testthat/copy-gh.R
tests/testthat/copy_gate.R
tests/testthat/cytoframe-suite.R
tests/testthat/cytoset-suite.R
tests/testthat/expect_result/cv_gh.rds
tests/testthat/expect_result/cv_gs.csv
tests/testthat/expect_result/empty_pop.rds
tests/testthat/expect_result/getAllDescendants_cd3_gh.rds
tests/testthat/expect_result/getAllDescendants_cd4_gh.rds
tests/testthat/expect_result/getAllDescendants_cd8_gh.rds
tests/testthat/expect_result/getAxisLabels_gh.rds
tests/testthat/expect_result/getCompensationMatrices_gh.rds
tests/testthat/expect_result/getData_COMPASS_gs.rds
tests/testthat/expect_result/getGate_gs.rds
tests/testthat/expect_result/getGate_gs_ellipse.rds
tests/testthat/expect_result/getGate_gs_polygon.rds
tests/testthat/expect_result/getGraph_gh.rds
tests/testthat/expect_result/getIndiceMat_gh.rds
tests/testthat/expect_result/getIndice_singlet_gh.rds
tests/testthat/expect_result/getIndices_gs.rds
tests/testthat/expect_result/getNodes_gh.rds
tests/testthat/expect_result/getPopStats_gh.csv
tests/testthat/expect_result/getPopStats_gs.csv
tests/testthat/expect_result/getTransformations_gh.rds
tests/testthat/expect_result/kw_gh.rds
tests/testthat/expect_result/kw_gs.rds
tests/testthat/expect_result/layoutGraph_gh.rds
tests/testthat/filter_to_list.R
tests/testthat/gh_pop_move.R
tests/testthat/gs-archive.R
tests/testthat/gs-parsed.R
tests/testthat/gs_pop_get_count_fast.R
tests/testthat/helper-expectResult.R
tests/testthat/helper_equal_function.R
tests/testthat/parallel_load_gs.R
tests/testthat/pop-add.R
tests/testthat/s3-gs.R
tests/testthat/scale_gate.R
tests/testthat/test-main.R
tests/testthat/write.FCS.R
vignettes/HowToMergeGatingSet.Rmd
vignettes/flowWorkspace-Introduction.Rmd
