Files in romanhaa/cerebroApp

Interactive visualization of scRNA-seq data with Cerebro

.Rbuildignore

.gitignore

DESCRIPTION

DISCONTINUATION_NOTICE.md

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/addPercentMtRibo.R R/calculatePercentGenes.R R/class-Cerebro_v1.3.R R/exportFromSCE.R R/exportFromSeurat.R R/extractMonocleTrajectory.R R/getEnrichedPathways.R R/getMarkerGenes.R R/getMostExpressedGenes.R R/launchCerebro.R R/launchCerebroV1.0.R R/launchCerebroV1.1.R R/launchCerebroV1.2.R R/launchCerebroV1.3.R R/performGeneSetEnrichmentAnalysis.R R/read_GMT_file.R R/send_enrichr_query.r README.md TODO.md

inst/CITATION

inst/NEWS

inst/app.R

inst/extdata/example_gene_set.gmt

inst/extdata/genes_mt_hg_ensembl.tsv.gz

inst/extdata/genes_mt_hg_gencode_v27.tsv.gz

inst/extdata/genes_mt_hg_name.tsv.gz

inst/extdata/genes_mt_mm_ensembl.tsv.gz

inst/extdata/genes_mt_mm_gencode_vM16.tsv.gz

inst/extdata/genes_mt_mm_name.tsv.gz

inst/extdata/genes_ribo_hg_ensembl.tsv.gz

inst/extdata/genes_ribo_hg_gencode_v27.tsv.gz

inst/extdata/genes_ribo_hg_name.tsv.gz

inst/extdata/genes_ribo_mm_ensembl.tsv.gz

inst/extdata/genes_ribo_mm_gencode_vM16.tsv.gz

inst/extdata/genes_ribo_mm_name.tsv.gz

inst/extdata/hg38_gene_ID_name.tsv.gz

inst/extdata/logo_Cerebro.png

inst/extdata/mm10_gene_ID_name.tsv.gz

inst/extdata/v1.0/example.rds

inst/extdata/v1.1/example.rds

inst/extdata/v1.2/example.rds

inst/extdata/v1.2/seurat_pbmc.rds

inst/extdata/v1.3/example.crb

inst/extdata/v1.3/pbmc_SCE.rds

inst/extdata/v1.3/pbmc_seurat.rds

inst/shiny/v1.0/about/UI.R inst/shiny/v1.0/about/server.R inst/shiny/v1.0/analysis_info/UI.R inst/shiny/v1.0/analysis_info/server.R inst/shiny/v1.0/clusters/UI.R inst/shiny/v1.0/clusters/info.R inst/shiny/v1.0/clusters/server.R inst/shiny/v1.0/enriched_pathways/UI.R inst/shiny/v1.0/enriched_pathways/info.R inst/shiny/v1.0/enriched_pathways/server.R inst/shiny/v1.0/gene_expression/UI.R inst/shiny/v1.0/gene_expression/info.R inst/shiny/v1.0/gene_expression/server.R inst/shiny/v1.0/gene_id_conversion/UI.R inst/shiny/v1.0/gene_id_conversion/info.R inst/shiny/v1.0/gene_id_conversion/server.R inst/shiny/v1.0/gene_set_expression/UI.R inst/shiny/v1.0/gene_set_expression/info.R inst/shiny/v1.0/gene_set_expression/server.R inst/shiny/v1.0/load_data/UI.R inst/shiny/v1.0/load_data/server.R inst/shiny/v1.0/marker_genes/UI.R inst/shiny/v1.0/marker_genes/info.R inst/shiny/v1.0/marker_genes/server.R inst/shiny/v1.0/most_expressed_genes/UI.R inst/shiny/v1.0/most_expressed_genes/info.R inst/shiny/v1.0/most_expressed_genes/server.R inst/shiny/v1.0/overview/UI.R inst/shiny/v1.0/overview/info.R inst/shiny/v1.0/overview/server.R inst/shiny/v1.0/samples/UI.R inst/shiny/v1.0/samples/info.R inst/shiny/v1.0/samples/server.R inst/shiny/v1.0/shiny_UI.R inst/shiny/v1.0/shiny_server.R inst/shiny/v1.1/about/UI.R inst/shiny/v1.1/about/server.R inst/shiny/v1.1/analysis_info/UI.R inst/shiny/v1.1/analysis_info/server.R inst/shiny/v1.1/clusters/UI.R inst/shiny/v1.1/clusters/info.R inst/shiny/v1.1/clusters/server.R inst/shiny/v1.1/enriched_pathways/UI.R inst/shiny/v1.1/enriched_pathways/info.R inst/shiny/v1.1/enriched_pathways/server.R inst/shiny/v1.1/gene_expression/UI.R inst/shiny/v1.1/gene_expression/info.R inst/shiny/v1.1/gene_expression/server.R inst/shiny/v1.1/gene_id_conversion/UI.R inst/shiny/v1.1/gene_id_conversion/info.R inst/shiny/v1.1/gene_id_conversion/server.R inst/shiny/v1.1/gene_set_expression/UI.R inst/shiny/v1.1/gene_set_expression/info.R inst/shiny/v1.1/gene_set_expression/server.R inst/shiny/v1.1/load_data/UI.R inst/shiny/v1.1/load_data/server.R inst/shiny/v1.1/marker_genes/UI.R inst/shiny/v1.1/marker_genes/info.R inst/shiny/v1.1/marker_genes/server.R inst/shiny/v1.1/most_expressed_genes/UI.R inst/shiny/v1.1/most_expressed_genes/info.R inst/shiny/v1.1/most_expressed_genes/server.R inst/shiny/v1.1/overview/UI.R inst/shiny/v1.1/overview/info.R inst/shiny/v1.1/overview/server.R inst/shiny/v1.1/samples/UI.R inst/shiny/v1.1/samples/info.R inst/shiny/v1.1/samples/server.R inst/shiny/v1.1/shiny_UI.R inst/shiny/v1.1/shiny_server.R inst/shiny/v1.1/trajectory/UI.R inst/shiny/v1.1/trajectory/info.R inst/shiny/v1.1/trajectory/server.R inst/shiny/v1.2/about/UI.R inst/shiny/v1.2/about/server.R inst/shiny/v1.2/analysis_info/UI.R inst/shiny/v1.2/analysis_info/server.R inst/shiny/v1.2/clusters/UI.R inst/shiny/v1.2/clusters/info.R inst/shiny/v1.2/clusters/server.R inst/shiny/v1.2/color_management/UI.R inst/shiny/v1.2/color_management/info.R inst/shiny/v1.2/color_management/server.R inst/shiny/v1.2/enriched_pathways/UI.R inst/shiny/v1.2/enriched_pathways/info.R inst/shiny/v1.2/enriched_pathways/server.R inst/shiny/v1.2/gene_expression/UI.R inst/shiny/v1.2/gene_expression/info.R inst/shiny/v1.2/gene_expression/server.R inst/shiny/v1.2/gene_id_conversion/UI.R inst/shiny/v1.2/gene_id_conversion/info.R inst/shiny/v1.2/gene_id_conversion/server.R inst/shiny/v1.2/gene_set_expression/UI.R inst/shiny/v1.2/gene_set_expression/info.R inst/shiny/v1.2/gene_set_expression/server.R inst/shiny/v1.2/load_data/UI.R inst/shiny/v1.2/load_data/server.R inst/shiny/v1.2/marker_genes/UI.R inst/shiny/v1.2/marker_genes/info.R inst/shiny/v1.2/marker_genes/server.R inst/shiny/v1.2/most_expressed_genes/UI.R inst/shiny/v1.2/most_expressed_genes/info.R inst/shiny/v1.2/most_expressed_genes/server.R inst/shiny/v1.2/overview/UI.R inst/shiny/v1.2/overview/info.R inst/shiny/v1.2/overview/server.R inst/shiny/v1.2/samples/UI.R inst/shiny/v1.2/samples/info.R inst/shiny/v1.2/samples/server.R inst/shiny/v1.2/shiny_UI.R inst/shiny/v1.2/shiny_server.R inst/shiny/v1.2/trajectory/UI.R inst/shiny/v1.2/trajectory/info.R inst/shiny/v1.2/trajectory/server.R inst/shiny/v1.3/about/UI.R inst/shiny/v1.3/about/server.R inst/shiny/v1.3/analysis_info/UI.R inst/shiny/v1.3/analysis_info/server.R inst/shiny/v1.3/color_management/UI.R inst/shiny/v1.3/color_management/server.R inst/shiny/v1.3/color_setup.R inst/shiny/v1.3/enriched_pathways/UI.R inst/shiny/v1.3/enriched_pathways/select_content.R inst/shiny/v1.3/enriched_pathways/server.R inst/shiny/v1.3/enriched_pathways/table.R inst/shiny/v1.3/extra_material/UI.R inst/shiny/v1.3/extra_material/content.R inst/shiny/v1.3/extra_material/select_content.R inst/shiny/v1.3/extra_material/server.R inst/shiny/v1.3/gene_expression/UI.R inst/shiny/v1.3/gene_expression/UI_expression_by_gene.R inst/shiny/v1.3/gene_expression/UI_expression_by_group.R inst/shiny/v1.3/gene_expression/UI_expression_by_pseudotime.R inst/shiny/v1.3/gene_expression/UI_expression_in_selected_cells.R inst/shiny/v1.3/gene_expression/UI_projection.R inst/shiny/v1.3/gene_expression/UI_projection_additional_parameters.R inst/shiny/v1.3/gene_expression/UI_projection_color_scale.R inst/shiny/v1.3/gene_expression/UI_projection_color_scale_range.R inst/shiny/v1.3/gene_expression/UI_projection_genes_separate_panels.R inst/shiny/v1.3/gene_expression/UI_projection_group_filters.R inst/shiny/v1.3/gene_expression/UI_projection_input_type.R inst/shiny/v1.3/gene_expression/UI_projection_point_border.R inst/shiny/v1.3/gene_expression/UI_projection_scales.R inst/shiny/v1.3/gene_expression/UI_projection_select_projection.R inst/shiny/v1.3/gene_expression/UI_table_of_selected_cells.R inst/shiny/v1.3/gene_expression/event_projection_export_plot.R inst/shiny/v1.3/gene_expression/event_projection_update_plot.R inst/shiny/v1.3/gene_expression/func_pltExpProj2DMultPanExp.R inst/shiny/v1.3/gene_expression/func_pltExpProj2DSglPanExp.R inst/shiny/v1.3/gene_expression/func_pltExpTrj2DSglPanExp.R inst/shiny/v1.3/gene_expression/func_projection_update_plot.R

inst/shiny/v1.3/gene_expression/js_projection_update_plot.js

inst/shiny/v1.3/gene_expression/obj_projection_cells_to_show.R inst/shiny/v1.3/gene_expression/obj_projection_coordinates.R inst/shiny/v1.3/gene_expression/obj_projection_data.R inst/shiny/v1.3/gene_expression/obj_projection_data_to_plot.R inst/shiny/v1.3/gene_expression/obj_projection_expression_levels.R inst/shiny/v1.3/gene_expression/obj_projection_hover_info.R inst/shiny/v1.3/gene_expression/obj_projection_parameters_color.R inst/shiny/v1.3/gene_expression/obj_projection_parameters_plot.R inst/shiny/v1.3/gene_expression/obj_projection_selected_cells.R inst/shiny/v1.3/gene_expression/obj_projection_trajectory.R inst/shiny/v1.3/gene_expression/obj_selected_genes.R inst/shiny/v1.3/gene_expression/out_genes_displayed.R inst/shiny/v1.3/gene_expression/out_number_of_selected_cells.R inst/shiny/v1.3/gene_expression/out_projection.R inst/shiny/v1.3/gene_expression/server.R inst/shiny/v1.3/gene_id_conversion/UI.R inst/shiny/v1.3/gene_id_conversion/server.R inst/shiny/v1.3/groups/UI.R inst/shiny/v1.3/groups/cell_cycle.R inst/shiny/v1.3/groups/composition.R inst/shiny/v1.3/groups/expression_metrics.R inst/shiny/v1.3/groups/select_group.R inst/shiny/v1.3/groups/server.R inst/shiny/v1.3/groups/tree.R inst/shiny/v1.3/load_data/UI.R inst/shiny/v1.3/load_data/sample_info.R inst/shiny/v1.3/load_data/select_file.R inst/shiny/v1.3/load_data/server.R inst/shiny/v1.3/marker_genes/UI.R inst/shiny/v1.3/marker_genes/select_content.R inst/shiny/v1.3/marker_genes/server.R inst/shiny/v1.3/marker_genes/table.R inst/shiny/v1.3/most_expressed_genes/UI.R inst/shiny/v1.3/most_expressed_genes/select_group.R inst/shiny/v1.3/most_expressed_genes/server.R inst/shiny/v1.3/most_expressed_genes/table.R inst/shiny/v1.3/overview/UI.R inst/shiny/v1.3/overview/UI_projection.R inst/shiny/v1.3/overview/UI_projection_additional_parameters.R inst/shiny/v1.3/overview/UI_projection_group_filters.R inst/shiny/v1.3/overview/UI_projection_main_parameters.R inst/shiny/v1.3/overview/UI_projection_point_border.R inst/shiny/v1.3/overview/UI_projection_scales.R inst/shiny/v1.3/overview/UI_projection_show_group_label.R inst/shiny/v1.3/overview/UI_selected_cells_plot.R inst/shiny/v1.3/overview/UI_selected_cells_table.R inst/shiny/v1.3/overview/event_projection_export_plot.R inst/shiny/v1.3/overview/event_projection_update_plot.R inst/shiny/v1.3/overview/func_projection_update_plot.R

inst/shiny/v1.3/overview/js_projection_update_plot.js

inst/shiny/v1.3/overview/obj_projection_cells_to_show.R inst/shiny/v1.3/overview/obj_projection_color_assignments.R inst/shiny/v1.3/overview/obj_projection_coordinates.R inst/shiny/v1.3/overview/obj_projection_data.R inst/shiny/v1.3/overview/obj_projection_data_to_plot.R inst/shiny/v1.3/overview/obj_projection_hover_info.R inst/shiny/v1.3/overview/obj_projection_parameters_plot.R inst/shiny/v1.3/overview/obj_projection_selected_cells.R inst/shiny/v1.3/overview/out_details_selected_cells_plot.R inst/shiny/v1.3/overview/out_details_selected_cells_table.R inst/shiny/v1.3/overview/out_number_of_selected_cells.R inst/shiny/v1.3/overview/out_projection.R inst/shiny/v1.3/overview/server.R inst/shiny/v1.3/plotting_functions.R inst/shiny/v1.3/shiny_UI.R inst/shiny/v1.3/shiny_server.R inst/shiny/v1.3/trajectory/UI.R inst/shiny/v1.3/trajectory/distribution_along_pseudotime.R inst/shiny/v1.3/trajectory/expression_metrics.R inst/shiny/v1.3/trajectory/number_of_expressed_genes_by_state.R inst/shiny/v1.3/trajectory/number_of_transcripts_by_state.R inst/shiny/v1.3/trajectory/projection.R inst/shiny/v1.3/trajectory/select_method_and_name.R inst/shiny/v1.3/trajectory/selected_cells_table.R inst/shiny/v1.3/trajectory/server.R inst/shiny/v1.3/trajectory/states_by_group.R inst/shiny/v1.3/utility_functions.R man/Cerebro_v1.3.Rd man/addPercentMtRibo.Rd man/calculatePercentGenes.Rd man/dot-read_GMT_file.Rd man/dot-send_enrichr_query.Rd man/exportFromSCE.Rd man/exportFromSeurat.Rd man/extractMonocleTrajectory.Rd man/getEnrichedPathways.Rd man/getMarkerGenes.Rd man/getMostExpressedGenes.Rd man/launchCerebro.Rd man/launchCerebroV1.0.Rd man/launchCerebroV1.1.Rd man/launchCerebroV1.2.Rd man/launchCerebroV1.3.Rd man/performGeneSetEnrichmentAnalysis.Rd other_documents/Cerebro_interface_v1.3.Rmd other_documents/benchmark_accessing_DelayedArray.Rmd

other_documents/benchmark_accessing_DelayedArray.html

other_documents/loading_cerebro_with_loaded_data_set.md other_documents/prepare_Cerebro_files_for_edge_cases.Rmd other_documents/prepare_cerebro_with_electricshine.Rmd other_documents/prepare_example_GMT_file.md other_documents/prepare_example_data_set.Rmd

other_documents/prepare_example_data_set.html

other_documents/prepare_gene_ID_name_conversion_tables.md other_documents/prepare_gene_lists.md other_documents/prepare_pbmc_example_with_SCE.Rmd

other_documents/prepare_pbmc_example_with_SCE.html

other_documents/prepare_pbmc_example_with_Seurat.Rmd

other_documents/prepare_pbmc_example_with_Seurat.html

other_documents/testing_prodecure_v1.3.Rmd other_documents/update_procedure.Rmd

pkgdown/_pkgdown.yml

vignettes/Cerebro_interface_v1.2.Rmd vignettes/cerebroApp_workflow_Seurat.Rmd vignettes/control_access_to_cerebro_with_a_login_page.Rmd vignettes/export_a_data_set_in_SCE_format.Rmd vignettes/export_and_visualize_custom_tables_and_plots.Rmd vignettes/host_cerebro_on_shinyapps.Rmd vignettes/launch_cerebro_with_pre-loaded_data_set.Rmd

vignettes/logo_Cerebro.png

vignettes/overview_of_cerebro_v1.3_class.Rmd vignettes/release_notes_v1.3.Rmd

romanhaa/cerebroApp documentation built on Nov. 25, 2021, 5:29 p.m.