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[docs] Add Rd files for the new functions.
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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^\.Rhistory$
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^docs$
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^LICENSE\.md$
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^doc$
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^Meta$
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^.github
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^.git
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^man/figures$
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_pkgdown\.yml
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vignettes
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cran-comments\.md
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^.*\.Rproj$
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^\.Rproj\.user$
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^\.Rhistory$
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^docs$
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^LICENSE\.md$
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^doc$
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^Meta$
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^.github
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^.git
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^man/figures$
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_pkgdown\.yml
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vignettes
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cran-comments\.md

‎.gitignore‎

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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src/*.o
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src/*.so
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src/*.dll
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/doc/
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/Meta/
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*tar.gz
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*Rcheck/
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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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src/*.o
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src/*.so
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src/*.dll
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/doc/
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/Meta/
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*tar.gz
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*Rcheck/

‎ClustAssess.Rproj‎

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source
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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes
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BuildType: Package
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PackageUseDevtools: Yes
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PackageInstallArgs: --no-multiarch --with-keep.source

‎LICENSE‎

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YEAR: 2020
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COPYRIGHT HOLDER: Arash Shahsavari
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YEAR: 2020
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COPYRIGHT HOLDER: Arash Shahsavari

‎LICENSE.md‎

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# MIT License
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Copyright (c) 2020 Arash Shahsavari
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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# MIT License
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Copyright (c) 2020 Arash Shahsavari
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎NAMESPACE‎

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# Generated by roxygen2: do not edit by hand
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S3method(write_shiny_app,Seurat)
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S3method(write_shiny_app,default)
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export(add_metadata)
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export(assess_clustering_stability)
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export(assess_feature_stability)
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export(assess_nn_stability)
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export(automatic_stability_assessment)
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export(calculate_markers)
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export(calculate_markers_shiny)
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export(choose_stable_clusters)
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export(consensus_cluster)
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export(create_monocle_default)
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export(create_monocle_from_clustassess)
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export(create_monocle_from_clustassess_app)
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export(create_seurat_object_default)
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export(create_seurat_object_from_clustassess_app)
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export(element_agreement)
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export(element_consistency)
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export(element_sim)
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export(element_sim_elscore)
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export(element_sim_matrix)
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export(getNNmatrix)
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export(get_clusters_from_clustassess_object)
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export(get_highest_prune_param)
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export(get_highest_prune_param_embedding)
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export(get_nn_conn_comps)
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export(marker_overlap)
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export(merge_partitions)
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export(pac_convergence)
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export(pac_landscape)
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export(plot_clustering_overall_stability)
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export(plot_clustering_per_value_stability)
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export(plot_connected_comps_evolution)
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export(plot_feature_overall_stability_boxplot)
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export(plot_feature_overall_stability_incremental)
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export(plot_feature_per_resolution_stability_boxplot)
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export(plot_feature_per_resolution_stability_incremental)
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export(plot_feature_stability_ecs_facet)
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export(plot_feature_stability_mb_facet)
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export(plot_k_n_partitions)
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export(plot_k_resolution_corresp)
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export(plot_n_neigh_ecs)
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export(plot_n_neigh_k_correspondence)
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export(server_comparisons)
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export(server_dimensionality_reduction)
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export(server_graph_clustering)
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export(server_graph_construction)
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export(server_landing_page)
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export(server_sandbox)
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export(ui_comparisons)
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export(ui_dimensionality_reduction)
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export(ui_graph_clustering)
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export(ui_graph_construction)
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export(ui_landing_page)
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export(ui_sandbox)
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export(weighted_element_consistency)
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export(write_objects)
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export(write_shiny_app)
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importClassesFrom(Matrix,Matrix)
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importFrom(dplyr,"%>%")
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importFrom(foreach,"%do%")
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importFrom(foreach,"%dopar%")
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importFrom(methods,new)
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importFrom(rlang,.data)
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useDynLib(ClustAssess)
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# Generated by roxygen2: do not edit by hand
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S3method(write_shiny_app,Seurat)
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S3method(write_shiny_app,default)
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export(add_metadata)
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export(assess_clustering_stability)
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export(assess_feature_stability)
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export(assess_nn_stability)
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export(automatic_stability_assessment)
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export(calculate_markers)
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export(calculate_markers_shiny)
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export(choose_stable_clusters)
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export(consensus_cluster)
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export(create_monocle_default)
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export(create_monocle_from_clustassess)
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export(create_monocle_from_clustassess_app)
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export(create_seurat_object_default)
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export(create_seurat_object_from_clustassess_app)
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export(element_agreement)
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export(element_consistency)
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export(element_sim)
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export(element_sim_elscore)
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export(element_sim_matrix)
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export(getNNmatrix)
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export(get_clusters_from_clustassess_object)
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export(get_highest_prune_param)
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export(get_highest_prune_param_embedding)
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export(get_nn_conn_comps)
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export(marker_overlap)
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export(merge_partitions)
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export(pac_convergence)
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export(pac_landscape)
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export(plot_clust_hierarchical)
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export(plot_clustering_overall_stability)
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export(plot_clustering_per_value_stability)
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export(plot_connected_comps_evolution)
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export(plot_feature_overall_stability_boxplot)
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export(plot_feature_overall_stability_incremental)
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export(plot_feature_per_resolution_stability_boxplot)
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export(plot_feature_per_resolution_stability_incremental)
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export(plot_feature_stability_ecs_facet)
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export(plot_feature_stability_mb_facet)
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export(plot_k_n_partitions)
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export(plot_k_resolution_corresp)
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export(plot_n_neigh_ecs)
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export(plot_n_neigh_k_correspondence)
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export(server_comparisons)
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export(server_dimensionality_reduction)
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export(server_graph_clustering)
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export(server_graph_construction)
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export(server_landing_page)
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export(server_sandbox)
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export(ui_comparisons)
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export(ui_dimensionality_reduction)
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export(ui_graph_clustering)
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export(ui_graph_construction)
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export(ui_landing_page)
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export(ui_sandbox)
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export(weighted_element_consistency)
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export(write_objects)
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export(write_shiny_app)
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importClassesFrom(Matrix,Matrix)
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importFrom(dplyr,"%>%")
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importFrom(foreach,"%do%")
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importFrom(foreach,"%dopar%")
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importFrom(methods,new)
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importFrom(rlang,.data)
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useDynLib(ClustAssess)

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