Package: omXplore 1.1.0
omXplore: Vizualization tools for 'omics' datasets with R
This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.
Authors:
omXplore_1.1.0.tar.gz
omXplore_1.1.0.zip(r-4.5)omXplore_1.1.0.zip(r-4.4)
omXplore_1.1.0.tgz(r-4.4-any)
omXplore_1.1.0.tar.gz(r-4.5-noble)omXplore_1.1.0.tar.gz(r-4.4-noble)
omXplore_1.1.0.tgz(r-4.4-emscripten)
omXplore.pdf |omXplore.html✨
omXplore/json (API)
NEWS
# Install 'omXplore' in R: |
install.packages('omXplore', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/prostarproteomics/omxplore/issues
On BioConductor:omXplore-0.99.8(bioc 3.20)
softwareshinyappsmassspectrometrydatarepresentationguiqualitycontrolprostar2
Last updated 2 days agofrom:89d574c450. Checks:OK: 1 WARNING: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | WARNING | Oct 31 2024 |
R-4.5-linux | WARNING | Oct 30 2024 |
R-4.4-win | WARNING | Oct 31 2024 |
R-4.4-mac | WARNING | Oct 31 2024 |
Exports:.initCompleteaddModulesboxPlotBuild_enriched_qdataBuild_X_CCBuildColorStylesbuildGraphCheck_MSnSet_ConsistencyCheck_se_ConsistencyChildrencolorLegendcolorLegend_servercolorLegend_uiconvert_to_maecorrMatrixcustom_metacell_colorscustomChartcustomExportMenuCVDistdensityPlotdf_to_maedf_to_sedisplay.CC.visNetExtendPaletteextFoo1extFoo1_serverextFoo1_uiextFoo2extFoo2_serverextFoo2_uiFormatDataForDTformatDTformatDT_serverformatDT_uiget_adjacencyMatrixget_ccget_colIDget_groupget_metacellget_parentProtIdget_pkg_versionget_typeGetCCInfosGetColorsForConditionsGetMetacellTagsGetPkgVersionglobalsheatmapDheatmapForMissingValuesis.listOflist_to_selistOfdf_to_maelistOfLists_to_maelistOfmatrix_to_maelistOfMSnSet_to_maelistOfSE_to_maelistPlotModuleslistShinyAppsMAE_Compatibility_with_Prostar_1xMAE_to_maematrix_to_maematrix_to_semetacell.defMSnSet_to_maeMSnSet_to_semv.heatmapomXplore_ccomXplore_cc_serveromXplore_cc_uiomXplore_corrmatrixomXplore_corrmatrix_serveromXplore_corrmatrix_uiomXplore_densityomXplore_density_serveromXplore_density_uiomXplore_heatmapomXplore_heatmap_serveromXplore_heatmap_uiomXplore_intensityomXplore_intensity_serveromXplore_intensity_uiomXplore_pcaomXplore_pca_serveromXplore_pca_uiomXplore_tabExploreromXplore_tabExplorer_serveromXplore_tabExplorer_uiomXplore_varianceomXplore_variance_serveromXplore_variance_uiParentpkgs.requireplotCCJitterplotPCA_EigenplotPCA_Eigen_hcplotPCA_IndplotPCA_Varplots_trackingplots_tracking_serverplots_tracking_uiQFeatures_to_maeSampleColorsSE_Compatibility_with_Prostar_1.xSE_to_maeview_datasetview_dataset_serverview_dataset_uiviolinPlotwrapper_pca
Dependencies:abindaffyaffyioAnnotationFilteraskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitopsbootbroombslibcachemcarcarDatacaToolscliclueclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydendextendDerivdigestdoBydoParalleldplyrDTellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapflashClustfontawesomeforeachformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegplotsgridExtragtablegtoolshighcharterhighrhtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleapslifecyclelimmalme4lubridatemagrittrMALDIquantMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrMsCoreUtilsMSnbasemultcompViewMultiAssayExperimentmunsellmvtnormmzIDmzRncdf4nlmenloptrnnetnumDerivopensslpbkrtestpcaMethodspillarpkgconfigplotlyplyrpolynompreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesquantmodquantregR6rappdirsRColorBrewerRcppRcppEigenreshape2Rhdf5librjsonrlangrlistrmarkdownrstatixS4ArraysS4Vectorssassscalesscatterplot3dshinyshinyBSshinyjquishinyjssmsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetinytexTTRUCSC.utilsutf8vctrsvioplotviridisviridisLitevisNetworkvsnwithrxfunXMLxtablextsXVectoryamlzlibbioczoo
Adding third party plots
Rendered fromaddingThirdPartyPlots.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2024-04-13
Started: 2024-03-11
omXplore: a versatile series of Shiny apps to explore 'omics' data
Rendered fromomXplore.Rmd
usingknitr::rmarkdown
on Oct 30 2024.Last update: 2024-04-13
Started: 2024-02-29
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Accessors functions | accessors get_adjacencyMatrix get_adjacencyMatrix,SummarizedExperiment-method get_cc get_cc,SummarizedExperiment-method get_colID get_colID,SummarizedExperiment-method get_group get_group,MultiAssayExperiment-method get_metacell get_metacell,SummarizedExperiment-method get_parentProtId get_parentProtId,SummarizedExperiment-method get_pkg_version get_pkg_version,SummarizedExperiment-method get_type get_type,SummarizedExperiment-method |
Builds enriched assay with cell metadata info | Build_enriched_qdata |
Build color style for DT tables | BuildColorStyles |
Color legend for DaparToolshed | color-legend colorLegend colorLegend_server colorLegend_ui custom_metacell_colors |
Convert to enriched MultiAssayExperiment | Build_X_CC Check_List_consistency Check_MSnSet_Consistency Check_se_Consistency Compute_CC converters convert_to_mae df_to_mae df_to_se listOfdf_to_mae listOfLists_to_mae listOfmatrix_to_mae listOfMSnSet_to_mae listOfSE_to_mae list_to_se MAE_to_mae matrix_to_mae matrix_to_se MSnSet_to_mae MSnSet_to_se QFeatures_to_mae SE_to_mae |
Displays a correlation matrix of the quantitative data of a numeric matrix. | corrMatrix corrmatrix omXplore_corrmatrix omXplore_corrmatrix_server omXplore_corrmatrix_ui |
Customised resetZoom Button of highcharts plots | customChart |
#' @title Customised contextual menu of highcharts plots | customExportMenu |
Displays a correlation matrix of the quantitative data of a numeric matrix. | density-plot densityPlot omXplore_density omXplore_density_server omXplore_density_ui |
Bar plot of missing values per lines using highcharter. | ds-pca omXplore_pca omXplore_pca_server omXplore_pca_ui plotPCA_Eigen plotPCA_Eigen_hc plotPCA_Ind plotPCA_Var wrapper_pca |
Bar plot of missing values per lines using 'highcharter'. | ds-view view_dataset view_dataset_server view_dataset_ui |
External module example | external_app extFoo1 extFoo1_server extFoo1_ui extFoo2 extFoo2_server extFoo2_ui |
formatDT_ui and formatDT_server | formatDT formatDT_server formatDT_ui format_DT |
Constructs a dataset suitable to use with the module format_DT. | FormatDataForDT |
Package version | GetPkgVersion |
Global variables | globals |
Displays different intensity plots. | boxPlot intensity-plots omXplore_intensity omXplore_intensity_server omXplore_intensity_ui violinPlot |
Checks the class of a list's slots | is.listOf |
Displays a correlation matrix of the quantitative data of a numeric matrix. | heatmapD heatmapForMissingValues mv.heatmap omXplore_heatmap omXplore_heatmap_server omXplore_heatmap_ui |
Explore 'MultiAssayExperiment' objects. | omXplore_tabExplorer omXplore_tabExplorer_server omXplore_tabExplorer_ui |
Shiny modules used by 'omXplore' | addModules listPlotModules listShinyApps omXplore-modules |
Palette for samples. | ExtendPalette GetColorsForConditions palette SampleColors |
Display a CC | buildGraph display.CC.visNet GetCCInfos pep_prot_CC plotCCJitter |
Loads packages | pkgs.require |
Variance plot | CVDist omXplore_variance omXplore_variance_server omXplore_variance_ui plot-variance |
Convert datasets exported by the package 'Prostar' | MAE_Compatibility_with_Prostar_1x Prostar-1x-compatible SE_Compatibility_with_Prostar_1.x |
Quantitative metadata vocabulary for entities | Children GetMetacellTags metacell.def Parent q_metadata |
Feature example data | sub_R25 |
Feature example data | vdata |