| across_picker_input |
Source code
|
| across_subset_picker_input |
Source code
|
| act_button |
Source code
|
| addClusterVariables |
Man page
Source code
|
| addHierarchicalClusterVariables |
Man page
Source code
|
| addKmeansClusterVariables |
Man page
Source code
|
| addMetaVariables |
Man page
Source code
|
| addPamClusterVariables |
Man page
Source code
|
| addStatVariables |
Man page
Source code
|
| addVariableSet |
Man page
Source code
|
| add_family |
Man page
Source code
|
| add_helper |
Man page
Source code
|
| add_vardenotation_to_cypro_object_shiny |
Man page
Source code
|
| adjustDefaultInstructions |
Man page
Source code
|
| adjust_well_roi_vec |
Man page
Source code
|
| adjust_well_vec |
Man page
Source code
|
| adjustableDefaultInstructions |
Man page
Source code
|
| agglomerateHierarchicalCluster |
Man page
Source code
|
| allColorpalettes |
Man page
|
| allColorspectra |
Man page
|
| all_of |
Man page
|
| animateAllTracks |
Man page
Source code
|
| animateWellImage |
Man page
Source code
|
| any_of |
Man page
|
| argument_dummy |
Man page
Source code
|
| assemble_additional_data_variables_module_info_shiny |
Man page
Source code
|
| assemble_analysis_module_info_shiny |
Man page
Source code
|
| assemble_id_module_info_shiny |
Man page
Source code
|
| assemble_tracks_one_time_imaging_shiny |
Man page
Source code
|
| assemble_tracks_time_lapse_shiny |
Man page
Source code
|
| assign_default |
Man page
Source code
|
| bar_position_picker_input |
Source code
|
| change_order_input |
Source code
|
| check_and_convert_grouping_var |
Source code
|
| check_and_convert_numeric_var |
Source code
|
| check_and_convert_vars_frame_num_and_cell_id |
Source code
|
| check_availability |
Man page
Source code
|
| check_df_variables |
Man page
Source code
|
| check_nrow |
Man page
Source code
|
| check_object |
Man page
Source code
|
| check_phase |
Man page
Source code
|
| check_phase_manually |
Man page
Source code
|
| check_renamed_variables |
Man page
Source code
|
| check_set_up_progress |
Man page
Source code
|
| check_summarize_with |
Man page
Source code
|
| check_track_df |
Man page
Source code
|
| check_wp_df_shiny |
Man page
Source code
|
| check_wp_directories |
Man page
Source code
|
| check_wp_name |
Man page
Source code
|
| checkpoint |
Man page
Source code
|
| clrp_picker_input |
Source code
|
| cluster_df_descr |
Man page
Source code
|
| color_to_picker_input |
Source code
|
| complete_stats |
Source code
|
| complete_tracks |
Man page
Source code
|
| computeDistanceMatrices |
Man page
Source code
|
| computeKmeansCluster |
Man page
Source code
|
| computePamCluster |
Man page
Source code
|
| compute_cell_stats |
Man page
Source code
|
| compute_distance |
Man page
Source code
|
| compute_distances_from_last_point |
Man page
Source code
|
| compute_distances_from_origin |
Man page
Source code
|
| compute_migration_efficiency |
Man page
Source code
|
| compute_module_variables |
Man page
Source code
|
| compute_n_missing_values |
Man page
Source code
|
| compute_stat |
Man page
Source code
|
| compute_zscore |
Source code
|
| contains |
Man page
|
| correlateAcross |
Man page
Source code
|
| correlateAll |
Man page
Source code
|
| css_status |
Man page
Source code
|
| designExperiment |
Man page
Source code
|
| detectBatchEffects |
Man page
Source code
|
| detectOutliers |
Man page
Source code
|
| detect_outliers_iqr |
Man page
Source code
|
| detect_outliers_mahalanobis |
Man page
Source code
|
| dim_red_df |
Man page
Source code
|
| discardClusterVariables |
Man page
Source code
|
| discardDistanceMatrix |
Man page
Source code
|
| discardMetaVariables |
Man page
Source code
|
| discardStatVariables |
Man page
Source code
|
| discardTrackVariables |
Man page
Source code
|
| ends_with |
Man page
|
| evaluate_file_availability_shiny |
Man page
Source code
|
| evaluate_file_content_shiny |
Man page
Source code
|
| example_selected |
Man page
Source code
|
| existOutlierResults |
Man page
Source code
|
| filterTracks |
Man page
Source code
|
| getAcrossOptions |
Man page
Source code
|
| getBatchEffectDf |
Man page
Source code
|
| getBatchEffectDist |
Man page
Source code
|
| getCellDf |
Source code
|
| getCellIds |
Man page
Source code
|
| getCellLines |
Man page
Source code
|
| getClusterDf |
Man page
Source code
|
| getClusterVariableNames |
Man page
Source code
|
| getConditions |
Man page
Source code
|
| getCorrConv |
Man page
Source code
|
| getCorrObject |
Man page
|
| getData |
Man page
Source code
|
| getDataFrame |
Man page
Source code
|
| getDefaultInstructions |
Source code
|
| getFrameLevels |
Source code
|
| getFrameSeq |
Source code
|
| getFrameTimeSeq |
Source code
|
| getGroupNames |
Man page
Source code
|
| getGroupingDf |
Man page
Source code
|
| getGroupingOptions |
Man page
Source code
|
| getGroupingVariableNames |
Man page
Source code
|
| getGroups |
Man page
Source code
Source code
|
| getHclustConv |
Man page
Source code
|
| getHclustObj |
Man page
Source code
|
| getHclustObject |
Man page
|
| getInterval |
Source code
|
| getIntervalUnit |
Source code
|
| getKmeansConv |
Man page
Source code
|
| getKmeansObject |
Man page
|
| getMetaDf |
Man page
Source code
|
| getMetaVariableNames |
Man page
Source code
|
| getMissingValuesDf |
Man page
Source code
|
| getNumericVariableNames |
Source code
|
| getOutlierIds |
Man page
Source code
|
| getOutlierResults |
Man page
Source code
|
| getOutlierWells |
Man page
Source code
|
| getPamConv |
Man page
Source code
|
| getPamObject |
Man page
|
| getPcaConv |
Man page
Source code
|
| getPcaObject |
Man page
|
| getPhases |
Source code
|
| getSetUpDf |
Man page
Source code
|
| getStatVariableNames |
Man page
Source code
|
| getStatsDf |
Man page
Source code
|
| getStatsOrTracksDf |
Source code
|
| getStorageDirectory |
Man page
Source code
|
| getSubsetList |
Source code
|
| getTrackVariableNames |
Man page
Source code
|
| getTracksDf |
Man page
Source code
|
| getTsneConv |
Man page
Source code
|
| getTsneObject |
Man page
|
| getUmapConv |
Man page
Source code
|
| getUmapObject |
Man page
|
| getVariableDf |
Man page
Source code
|
| getVariableSet |
Man page
Source code
|
| getVariableSetNames |
Man page
Source code
|
| getVariableSets |
Man page
Source code
|
| getVariableValues |
Man page
Source code
|
| getWellPlateDf |
Man page
Source code
|
| getWellPlateNames |
Man page
Source code
|
| getWellPlateVariableNames |
Man page
Source code
|
| get_all_var_name_pairs |
Source code
|
| get_computable_variable_names |
Source code
|
| get_denoted_variable_names |
Source code
|
| get_dim_red_obj |
Man page
Source code
|
| get_not_denoted_variable_names |
Source code
|
| get_used_module_names |
Source code
|
| get_variable_names_to_be_computed |
Source code
|
| ggplot_family |
Man page
Source code
Source code
|
| ggplot_return |
Man page
Source code
|
| ggpubr_comparison_list |
Man page
Source code
|
| ggpubr_y_labels |
Man page
Source code
|
| hlpr_add_data_to_cluster_object |
Man page
Source code
|
| hlpr_add_variable_specific_args |
Man page
Source code
|
| hlpr_add_vset_suffix |
Man page
Source code
|
| hlpr_assemble_df |
Man page
Source code
|
| hlpr_assemble_directory |
Man page
Source code
|
| hlpr_caption_add_on |
Man page
Source code
|
| hlpr_coords_flip_add_on |
Man page
Source code
|
| hlpr_create_meta_data |
Man page
Source code
|
| hlpr_create_track_list |
Man page
Source code
|
| hlpr_discard_messages_missing |
Man page
Source code
|
| hlpr_glue_phase |
Man page
Source code
|
| hlpr_keep_messages |
Man page
Source code
|
| hlpr_merge_condition_by_id |
Man page
Source code
|
| hlpr_merge_conditions |
Man page
Source code
|
| hlpr_module_name_pairs |
Man page
Source code
|
| hlpr_order_input |
Man page
Source code
|
| hlpr_phase_vertical_line |
Man page
Source code
|
| hlpr_plot_well_plate_fill |
Man page
Source code
|
| hlpr_pretty_colnames |
Man page
Source code
|
| hlpr_pretty_value |
Man page
Source code
|
| hlpr_pretty_vec |
Man page
Source code
|
| hlpr_process_tracks |
Man page
Source code
|
| hlpr_rename_df_cols |
Man page
Source code
|
| hlpr_select |
Man page
Source code
|
| hlpr_select_stats |
Man page
Source code
|
| hlpr_split_subset |
Man page
Source code
|
| hlpr_subset_across |
Man page
Source code
|
| hlpr_wp_ambiguous_number |
Man page
|
| hlpr_wp_ambiguous_number_f |
Man page
Source code
|
| hlpr_wp_directories |
Man page
Source code
|
| hlpr_wp_exp_file_number |
Man page
Source code
|
| hlpr_wp_file_number |
Man page
|
| hlpr_wp_file_number_f |
Man page
Source code
|
| hs |
Man page
Source code
|
| initiateCorrelation |
Man page
Source code
|
| initiateEmptyCyproObject |
Man page
Source code
|
| initiateHierarchicalClustering |
Man page
Source code
|
| initiateKmeansClustering |
Man page
Source code
|
| initiatePamClustering |
Man page
Source code
|
| input_df |
Man page
Source code
|
| isNormalizedWithZscore |
Man page
Source code
|
| isTimeLapseExp |
Man page
Source code
|
| isUsable |
Man page
Source code
|
| is_grouping_candidate |
Source code
|
| is_modified_wp_df |
Man page
Source code
|
| is_numeric_candidate |
Source code
|
| join_well_plate_data_and_input_one_time_imaging_shiny |
Source code
|
| join_well_plate_data_and_input_timelapse_shiny |
Source code
|
| join_with_meta |
Source code
|
| keepStatVariables |
Man page
Source code
|
| keepTrackVariables |
Man page
Source code
|
| labelsXremove |
Man page
Source code
|
| labelsXrotate |
Man page
Source code
|
| labelsYremove |
Man page
Source code
|
| labelsYrotate |
Man page
Source code
|
| legendBottom |
Man page
|
| legendNone |
Man page
|
| legendRight |
Man page
|
| legendTop |
Man page
|
| loadDataFile |
Man page
Source code
|
| loadDataFiles |
Man page
Source code
|
| load_data_files_shiny |
Man page
Source code
|
| loading_status_table_shiny |
Man page
Source code
|
| make_cutting_line |
Source code
|
| make_data_quality_reasoning |
Source code
|
| make_footer |
Source code
|
| make_header |
Source code
|
| make_module_heading |
Source code
|
| make_module_html |
Source code
|
| make_module_variable_pickers |
Source code
|
| make_phase |
Source code
|
| make_usage_switcher |
Source code
|
| matches |
Man page
|
| moduleExperimentDesignServer |
Man page
Source code
|
| moduleExperimentDesignUI |
Man page
Source code
|
| moduleLoadDataFileServer |
Man page
Source code
|
| moduleLoadDataFileUI |
Man page
Source code
|
| moduleLoadDataServer |
Man page
Source code
|
| moduleLoadDataUI |
Man page
Source code
|
| moduleQualityCheckServer |
Man page
Source code
|
| moduleQualityCheckUI |
Man page
Source code
|
| multiplePhases |
Man page
Source code
|
| mutateClusterDf |
Man page
Source code
|
| mutateMetaDf |
Man page
Source code
|
| mutateStatsDf |
Man page
Source code
|
| mutateTracksDf |
Man page
Source code
|
| mutate_cdata_slot |
Source code
|
| mutate_cell_df |
Source code
|
| nCellLines |
Man page
Source code
|
| nCells |
Man page
Source code
|
| nConditions |
Man page
Source code
|
| nFiles |
Man page
Source code
|
| nMissingValuesStats |
Man page
Source code
|
| nMissingValuesTracks |
Man page
Source code
|
| n_cells_numeric_input |
Source code
|
| normalizeZscore |
Man page
Source code
|
| numeric_variables_picker_input |
Source code
|
| organize_picker_input_in_rows |
Source code
|
| pdl_step_2_identifier_variables_html |
Source code
|
| pdl_step_3_module_variables_html |
Source code
|
| pdl_step_4_additional_variables_html |
Source code
|
| phase_cluster_picker_input |
Source code
|
| phase_picker_input |
Source code
|
| plotAllTracks |
Man page
Source code
|
| plotAvgSilhouetteWidths |
Man page
Source code
|
| plotBarchart |
Man page
Source code
|
| plotBatchHeatmap |
Man page
Source code
|
| plotBoxplot |
Man page
Source code
|
| plotCellCount |
Man page
Source code
|
| plotCorrelationSD |
Man page
Source code
|
| plotCorrplot |
Man page
Source code
|
| plotDendrogram |
Man page
Source code
|
| plotDensityplot |
Man page
Source code
|
| plotDimRed |
Man page
Source code
|
| plotDistribution |
Man page
Source code
|
| plotDistributionDiscrete |
Man page
Source code
|
| plotHeatmap |
Man page
Source code
|
| plotHistogram |
Man page
Source code
|
| plotPamMedoids |
Man page
Source code
|
| plotPca |
Man page
Source code
|
| plotRidgeplot |
Man page
Source code
|
| plotRosePlot |
Man page
|
| plotScatterplot |
Man page
Source code
|
| plotScreeplot |
Man page
Source code
|
| plotSilhouetteWidths |
Man page
Source code
|
| plotSingleTracks |
Man page
Source code
|
| plotStatisticsInteractive |
Man page
Source code
|
| plotTimeHeatmap |
Man page
Source code
|
| plotTimeLineplot |
Man page
Source code
|
| plotTsne |
Man page
Source code
|
| plotUmap |
Man page
Source code
|
| plotVelocityLineplot |
Man page
Source code
|
| plotViolinplot |
Man page
Source code
|
| plotWellPlate |
Man page
Source code
|
| plot_and_save |
Source code
|
| plot_dim_red |
Man page
Source code
|
| plot_qc_barplot_shiny |
Man page
Source code
|
| plot_qc_histogram_shiny |
Man page
Source code
|
| plot_well_plate_shiny |
Man page
Source code
|
| printAnalysisSummary |
Man page
|
| printSubsetHistory |
Man page
Source code
|
| printSummary |
Man page
Source code
|
| processData |
Man page
Source code
|
| protectedVariables |
Man page
Source code
|
| quality_check_summary_shiny |
Man page
Source code
|
| read_data_files_shiny |
Man page
Source code
|
| read_example_file_shiny |
Man page
Source code
|
| read_table_shiny |
Man page
Source code
|
| removeOutliers |
Man page
Source code
|
| renameClusterDf |
Man page
Source code
|
| renameClusterDfWith |
Man page
Source code
|
| renameGroups |
Man page
Source code
|
| renameMetaDf |
Man page
Source code
|
| renameMetaDfWith |
Man page
Source code
|
| renameStatsDf |
Man page
Source code
|
| renameStatsDfWith |
Man page
Source code
|
| renameTracksDf |
Man page
Source code
|
| renameTracksDfWith |
Man page
Source code
|
| rename_analysis_slots |
Source code
|
| rename_analysis_slots_with |
Source code
|
| runPca |
Man page
Source code
|
| runTsne |
Man page
Source code
|
| runUmap |
Man page
Source code
|
| run_dim_red |
Man page
Source code
|
| saveCyproObject |
Man page
Source code
|
| setCellDf |
Man page
Source code
|
| setClusterConv |
Man page
Source code
|
| setCorrConv |
Man page
Source code
|
| setDefaultInstructions |
Man page
Source code
|
| setDimRedConv |
Man page
Source code
|
| setGroupingDf |
Man page
Source code
|
| setStorageDirectory |
Man page
Source code
|
| setUpWellPlateDf |
Man page
Source code
|
| set_up_cdata_cluster |
Source code
|
| set_up_cdata_meta |
Source code
|
| set_up_cdata_stats |
Source code
|
| set_up_cdata_tracks |
Source code
|
| set_up_cdata_tracks_and_stats |
Source code
|
| set_up_cdata_well_plate |
Source code
|
| set_up_vdata |
Man page
Source code
|
| shiny_fdb |
Man page
Source code
|
| starts_with |
Man page
|
| subsetByCellId |
Man page
Source code
|
| subsetByCellLine |
Man page
Source code
|
| subsetByCluster |
Man page
Source code
|
| subsetByCondition |
Man page
Source code
|
| subsetByFilter |
Man page
Source code
|
| subsetByGroup |
Man page
Source code
|
| subsetByNumber |
Man page
Source code
|
| subsetByQuality |
Man page
Source code
|
| subset_history_cell_id |
Source code
|
| subset_history_cell_lines |
Source code
|
| subset_history_cluster |
Source code
|
| subset_history_conditions |
Source code
|
| subset_history_filter |
Source code
|
| subset_history_group |
Source code
|
| subset_history_number |
Source code
|
| subset_history_quality_check |
Source code
|
| summarizeTrackDfWith |
Man page
Source code
|
| summarize_module_variables |
Man page
|
| summarize_track_df |
Source code
|
| time_displaced_tmt |
Source code
|
| updateCyproObject |
Man page
Source code
|
| update_condition |
Man page
Source code
|
| update_condition_df |
Man page
Source code
|
| update_object |
Man page
Source code
|
| updated_object |
Man page
Source code
|
| used_variable_names_shiny |
Man page
Source code
|
| validAgglomerationMethods |
Man page
Source code
|
| validColorPalettes |
Man page
Source code
|
| validColorSpectra |
Man page
Source code
|
| validDistanceMethods |
Man page
Source code
|
| validKmeansMethods |
Man page
Source code
|
| valid_example_cols |
Man page
Source code
|
| validate_additional_variables_shiny |
Man page
Source code
|
| validate_analysis_module_variables_shiny |
Man page
Source code
|
| validate_identifier_variables_shiny |
Man page
Source code
|
| validate_timedisplaced_tmt |
Source code
|
| variable_description |
Source code
|
| variable_picker |
Source code
|
| variables_num |
Man page
Source code
|
| well_panel |
Source code
|
