Files in theMILOlab/cypro
A Toolbox for Analysis of Single Cell Microscopy Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/S4-documentation.R
R/add-family.R
R/animate-family.R
R/batch-effect-detection.R
R/check-family.R
R/checkpoint.R
R/clustering-hierarchical.R
R/clustering-initiation.R
R/clustering-kmeans.R
R/clustering-pam.R
R/complete-family.R
R/compute-family.R
R/correlation-analysis.R
R/cypro-modules-computation-aid.R
R/cypro-modules-miscellaneous.R
R/cypro-modules.R
R/default-instructions.R
R/deprecated.R
R/dimensional-reduction.R
R/discard-family.R
R/documentation-dummies.R
R/get-family.R
R/ggplot2-helper.R
R/helper-family.R
R/imported-functions.R
R/loading-and-saving.R
R/logical-tests.R
R/miscellaneous.R
R/mutate-data-frames.R
R/n-functions.R
R/normalization.R
R/object-initiation.R
R/outlier-detection.R
R/plot-family-statistics.R
R/plot-miscellaneous.R
R/plot-module-migration.R
R/plot-time-lapse.R
R/predefined-shiny-widgets.R
R/print-subset-history.R
R/print-summary.R
R/r-objects.R
R/rename-content.R
R/set-family.R
R/set-up-family.R
R/shiny-functions.R
R/shiny-html-generating-functions.R
R/shiny-module-design-experiment-server.R
R/shiny-module-design-experiment-ui.R
R/shiny-module-load-data-by-file-server-helper.R
R/shiny-module-load-data-by-file-server.R
R/shiny-module-load-data-by-file-ui.R
R/shiny-module-load-data-server.R
R/shiny-module-load-data-ui.R
R/shiny-module-quality-check-server.R
R/shiny-module-quality-check-ui.R
R/statistic-functions.R
R/subset-object.R
R/summarize-timelapse-data.R
R/update-cypro-object.R
R/valid-input-options.R
README.md
_pkgdown.yml
cypro.Rproj
docs/404.html
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docs/reference/plotBoxplot.html
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docs/reference/plotCorrelationSD.html
docs/reference/plotCorrplot.html
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docs/reference/plotSingleTracks.html
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docs/reference/plotTimeLineplot.html
docs/reference/plotVelocityLineplot.html
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docs/reference/removeOutliers.html
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docs/reference/renameGroups.html
docs/reference/renameMetaDf.html
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docs/reference/renameTracksDf.html
docs/reference/runPca.html
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docs/reference/saveCyproObject.html
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docs/reference/setClusterConv.html
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docs/reference/set_up_vdata.html
docs/reference/shiny_fdb.html
docs/reference/starts_with.html
docs/reference/subsetByCellId.html
docs/reference/subsetByCellLine.html
docs/reference/subsetByCluster.html
docs/reference/subsetByCondition.html
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docs/reference/subsetByNumber.html
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docs/reference/summarizeTrackDfWith.html
docs/reference/updateCyproObject.html
docs/reference/update_condition.html
docs/reference/updated_object.html
docs/reference/used_variable_names_shiny.html
docs/reference/validAgglomerationMethods.html
docs/reference/valid_example_cols.html
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docs/reference/validate_analysis_module_variables_shiny.html
docs/reference/validate_identifier_variables_shiny.html
docs/reference/variables_num.html
docs/sitemap.xml
docs/styles.css
man/addClusterVariables.Rd
man/addHierarchicalClusterVariables.Rd
man/addKmeansClusterVariables.Rd
man/addPamClusterVariables.Rd
man/addStatVariables.Rd
man/addVariableSet.Rd
man/add_family.Rd
man/add_helper.Rd
man/add_vardenotation_to_cypro_object_shiny.Rd
man/adjustDefaultInstructions.Rd
man/adjust_well_roi_vec.Rd
man/adjust_well_vec.Rd
man/adjustableDefaultInstructions.Rd
man/agglomerateHierarchicalCluster.Rd
man/allColorpalettes.Rd
man/animateAllTracks.Rd
man/animateWellImage.Rd
man/argument_dummy.Rd
man/assemble_additional_data_variables_module_info_shiny.Rd
man/assemble_analysis_module_info_shiny.Rd
man/assemble_id_module_info_shiny.Rd
man/assemble_tracks_one_time_imaging_shiny.Rd
man/assemble_tracks_time_lapse_shiny.Rd
man/assign_default.Rd
man/check_availability.Rd
man/check_df_variables.Rd
man/check_nrow.Rd
man/check_object.Rd
man/check_phase.Rd
man/check_phase_manually.Rd
man/check_renamed_variables.Rd
man/check_set_up_progress.Rd
man/check_summarize_with.Rd
man/check_track_df.Rd
man/check_wp_df_shiny.Rd
man/check_wp_directories.Rd
man/check_wp_name.Rd
man/checkpoint.Rd
man/cluster_df_descr.Rd
man/complete_tracks.Rd
man/computeDistanceMatrices.Rd
man/computeKmeansCluster.Rd
man/computePamCluster.Rd
man/compute_cell_stats.Rd
man/compute_distance.Rd
man/compute_distances_from_origin.Rd
man/compute_migration_efficiency.Rd
man/compute_module_variables.Rd
man/compute_n_missing_values.Rd
man/correlateAll.Rd
man/css_status.Rd
man/designExperiment.Rd
man/detectBatchEffects.Rd
man/detectOutliers.Rd
man/detect_outliers_iqr.Rd
man/dim_red_df.Rd
man/discardClusterVariables.Rd
man/discardDistanceMatrix.Rd
man/discardStatVariables.Rd
man/evaluate_file_availability_shiny.Rd
man/example_selected.Rd
man/existOutlierResults.Rd
man/filterTracks.Rd
man/getBatchEffectDf.Rd
man/getCellIds.Rd
man/getCellLines.Rd
man/getCorrConv.Rd
man/getData.Rd
man/getDataFrame.Rd
man/getGroupNames.Rd
man/getGroupingDf.Rd
man/getGroupingOptions.Rd
man/getGroupingVariableNames.Rd
man/getHclustConv.Rd
man/getHclustObj.Rd
man/getMissingValuesDf.Rd
man/getOutlierResults.Rd
man/getOutlierWells.Rd
man/getPcaConv.Rd
man/getSetUpDf.Rd
man/getStatVariableNames.Rd
man/getStatsDf.Rd
man/getStorageDirectory.Rd
man/getTracksDf.Rd
man/getVariableDf.Rd
man/getVariableSet.Rd
man/getVariableValues.Rd
man/getWellPlateNames.Rd
man/get_dim_red_obj.Rd
man/ggplot_family.Rd
man/ggplot_return.Rd
man/ggpubr_comparison_list.Rd
man/hlpr_add_data_to_cluster_object.Rd
man/hlpr_add_variable_specific_args.Rd
man/hlpr_add_vset_suffix.Rd
man/hlpr_assemble_df.Rd
man/hlpr_assemble_directory.Rd
man/hlpr_caption_add_on.Rd
man/hlpr_coords_flip_add_on.Rd
man/hlpr_create_meta_data.Rd
man/hlpr_create_track_list.Rd
man/hlpr_glue_phase.Rd
man/hlpr_keep_messages.Rd
man/hlpr_merge_conditions.Rd
man/hlpr_module_name_pairs.Rd
man/hlpr_order_input.Rd
man/hlpr_phase_vertical_line.Rd
man/hlpr_pretty_colnames.Rd
man/hlpr_process_tracks.Rd
man/hlpr_rename_df_cols.Rd
man/hlpr_select_stats.Rd
man/hlpr_split_subset.Rd
man/hlpr_subset_across.Rd
man/hlpr_wp_directories.Rd
man/hs.Rd
man/initiateCorrelation.Rd
man/initiateEmptyCyproObject.Rd
man/initiateHierarchicalClustering.Rd
man/input_df.Rd
man/is_modified_wp_df.Rd
man/labelsXrotate.Rd
man/legendBottom.Rd
man/loadDataFile.Rd
man/load_data_files_shiny.Rd
man/loading_status_table_shiny.Rd
man/moduleExperimentDesignServer.Rd
man/moduleExperimentDesignUI.Rd
man/moduleLoadDataFileServer.Rd
man/moduleLoadDataFileUI.Rd
man/moduleLoadDataServer.Rd
man/moduleLoadDataUI.Rd
man/moduleQualityCheckServer.Rd
man/moduleQualityCheckUI.Rd
man/mutateClusterDf.Rd
man/mutateTracksDf.Rd
man/nCells.Rd
man/nFiles.Rd
man/nMissingValuesStats.Rd
man/nMissingValuesTracks.Rd
man/normalizeZscore.Rd
man/plotAllTracks.Rd
man/plotAvgSilhouetteWidths.Rd
man/plotBarchart.Rd
man/plotBatchHeatmap.Rd
man/plotBoxplot.Rd
man/plotCellCount.Rd
man/plotCorrelationSD.Rd
man/plotCorrplot.Rd
man/plotDendrogram.Rd
man/plotDimRed.Rd
man/plotDistribution.Rd
man/plotDistributionDiscrete.Rd
man/plotHeatmap.Rd
man/plotPamMedoids.Rd
man/plotPca.Rd
man/plotScatterplot.Rd
man/plotScreeplot.Rd
man/plotSingleTracks.Rd
man/plotStatisticsInteractive.Rd
man/plotTimeHeatmap.Rd
man/plotTimeLineplot.Rd
man/plotVelocityLineplot.Rd
man/plotWellPlate.Rd
man/plot_dim_red.Rd
man/plot_qc_barplot_shiny.Rd
man/plot_qc_histogram_shiny.Rd
man/plot_well_plate_shiny.Rd
man/printSubsetHistory.Rd
man/printSummary.Rd
man/processData.Rd
man/protectedVariables.Rd
man/quality_check_summary_shiny.Rd
man/read_data_files_shiny.Rd
man/read_example_file_shiny.Rd
man/read_table_shiny.Rd
man/removeOutliers.Rd
man/renameClusterDf.Rd
man/renameGroups.Rd
man/renameMetaDf.Rd
man/renameStatsDf.Rd
man/renameTracksDf.Rd
man/runPca.Rd
man/run_dim_red.Rd
man/saveCyproObject.Rd
man/setCellDf.Rd
man/setClusterConv.Rd
man/setDefaultInstructions.Rd
man/setGroupingDf.Rd
man/setStorageDirectory.Rd
man/setUpWellPlateDf.Rd
man/set_up_vdata.Rd
man/shiny_fdb.Rd
man/starts_with.Rd
man/subsetByCellId.Rd
man/subsetByCellLine.Rd
man/subsetByCluster.Rd
man/subsetByCondition.Rd
man/subsetByFilter.Rd
man/subsetByNumber.Rd
man/subsetByQuality.Rd
man/summarizeTrackDfWith.Rd
man/updateCyproObject.Rd
man/update_condition.Rd
man/updated_object.Rd
man/used_variable_names_shiny.Rd
man/validAgglomerationMethods.Rd
man/valid_example_cols.Rd
man/validate_additional_variables_shiny.Rd
man/validate_analysis_module_variables_shiny.Rd
man/validate_identifier_variables_shiny.Rd
man/variables_num.Rd
notes/cp-regex.R
