Package: omXplore 1.7.0

Samuel Wieczorek

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:Samuel Wieczorek [aut, cre], Thomas Burger [aut], Enora Fremy [ctb], Cyril Ariztegui [ctb], Manon Gaudin [ctb]

omXplore_1.7.0.tar.gz
omXplore_1.7.0.zip(r-4.7)omXplore_1.7.0.zip(r-4.6)omXplore_1.7.0.zip(r-4.5)
omXplore_1.7.0.tgz(r-4.6-any)omXplore_1.7.0.tgz(r-4.5-any)
omXplore_1.7.0.tar.gz(r-4.7-any)omXplore_1.7.0.tar.gz(r-4.6-any)
omXplore_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/edyp-lab/omxplore/issues

Pkgdown/docs site:https://edyp-lab.github.io

Datasets:

sub_R25 - Feature example data
vdata - Feature example data

On BioConductor:omXplore-1.7.0(bioc 3.24)omXplore-1.6.0(bioc 3.23)

software shinyapps massspectrometry datarepresentation gui qualitycontrol prostar2

5.36 score 38 scripts 302 downloads 109 exports 199 dependencies

Last updated from:2b3acd9f97. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	258
linux-devel-x86_64	WARNING	462
source / vignettes	OK	338
linux-release-x86_64	WARNING	435
macos-release-arm64	WARNING	324
macos-oldrel-arm64	WARNING	276
windows-devel	WARNING	341
windows-release	WARNING	399
windows-oldrel	WARNING	365
wasm-release	OK	194

Exports:.initComplete addModules boxPlot Build_enriched_qdata Build_X_CC BuildColorStyles buildGraph Check_MSnSet_Consistency Check_se_Consistency Children colorLegend colorLegend_server colorLegend_ui convert_to_mae corrMatrix custom_metacell_colors CVDist densityPlot df_to_mae df_to_se display.CC.visNet ExtendPalette extFoo1 extFoo1_server extFoo1_ui extFoo2 extFoo2_server extFoo2_ui FormatDataForDT formatDT formatDT_server formatDT_ui get_adjacencyMatrix get_cc get_colID get_design get_group get_metacell get_parentProtId get_pkg_version get_type GetCCInfos GetColorsForConditions GetMetacellTags GetPkgVersion globals heatmapD heatmapForMissingValues is.listOf list_to_se listOfdf_to_mae listOfLists_to_mae listOfmatrix_to_mae listOfMSnSet_to_mae listOfSE_to_mae listPlotModules listShinyApps MAE_Compatibility_with_Prostar_1x MAE_to_mae matrix_to_mae matrix_to_se metacell.def MSnSet_to_mae MSnSet_to_se mv.heatmap my_PCA omXplore_cc omXplore_cc_server omXplore_cc_ui omXplore_corrmatrix omXplore_corrmatrix_server omXplore_corrmatrix_ui omXplore_density omXplore_density_server omXplore_density_ui omXplore_heatmap omXplore_heatmap_server omXplore_heatmap_ui omXplore_intensity omXplore_intensity_server omXplore_intensity_ui omXplore_pca omXplore_pca_server omXplore_pca_ui omXplore_tabExplorer omXplore_tabExplorer_server omXplore_tabExplorer_ui omXplore_variance omXplore_variance_server omXplore_variance_ui Parent pkgs.require2 plotCCJitter plotPCA_Eigen plotPCA_Eigen_hc plotPCA_Ind plotPCA_Var plots_tracking plots_tracking_server plots_tracking_ui QFeatures_to_mae SampleColors SE_Compatibility_with_Prostar_1.x SE_to_mae view_dataset view_dataset_server view_dataset_ui violinPlot wrapper_pca

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics biocmake BiocManager BiocParallel bitops boot broom bslib cachem car carData caTools cli clue cluster codetools colorspace commonmark corrplot cowplot cpp11 crosstalk curl data.table DelayedArray dendextend Deriv digest dir.expiry doBy doParallel dplyr DT ellipse emmeans estimability evaluate factoextra FactoMineR farver fastmap filelock flashClust fontawesome foreach forecast formatR Formula fracdiff fs futile.logger futile.options generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gplots gridExtra gtable gtools highr htmltools htmlwidgets httpuv httr igraph impute IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lmtest magrittr MALDIquant MASS Matrix MatrixGenerics MatrixModels matrixStats memoise MetaboCoreUtils mgcv microbenchmark mime minqa modelr MsCoreUtils MSnbase multcompView MultiAssayExperiment mvtnorm mzID mzR ncdf4 nipals nlme nloptr nnet numDeriv openssl otel pbkrtest pcaMethods pillar pkgconfig plotly plyr polynom preprocessCore promises ProtGenerics PSMatch PTMods purrr QFeatures quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 Rhdf5lib rlang rmarkdown rstatix S4Arrays S4Vectors S7 sass scales scatterplot3d Seqinfo shiny shinyBS shinyjqui shinyjs sm snow sourcetools SparseArray SparseM Spectra statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs vioplot viridis viridisLite visNetwork vsn withr xfun XML xtable XVector yaml zoo

Adding third party plots

Samuel Wieczorek, Thomas Burger

Rendered fromaddingThirdPartyPlots.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-04-15
Started: 2024-03-11

omXplore: a versatile series of Shiny apps to explore 'omics' data

Samuel Wieczorek, Thomas Burger

Rendered fromomXplore.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-04-21
Started: 2024-02-29

Citation

Development and contributors

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_design get_design,MultiAssayExperiment-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
Displays a correlation matrix of the quantitative data of a numeric matrix.	density-plot densityPlot omXplore_density omXplore_density_server omXplore_density_ui
my_PCA	ds-pca my_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 'plotly'.	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.require2
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