Package: omXplore 1.1.0

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]

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

Pkgdown site:https://prostarproteomics.github.io

Datasets:

sub_R25 - Feature example data
vdata - Feature example data

On BioConductor:omXplore-1.1.0(bioc 3.21)omXplore-1.0.0(bioc 3.20)

software shinyapps massspectrometry datarepresentation gui qualitycontrol prostar2

5.23 score 19 scripts 109 exports 196 dependencies

Last updated 2 months agofrom:89d574c450. Checks:OK: 1 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 03 2024
R-4.5-win	WARNING	Dec 03 2024
R-4.5-linux	WARNING	Dec 03 2024
R-4.4-win	WARNING	Dec 03 2024
R-4.4-mac	WARNING	Dec 03 2024

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 customChart customExportMenu 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_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 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.require 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 assertthat backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel bitops boot broom bslib cachem car carData caTools cli clue cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray dendextend Deriv digest doBy doParallel dplyr DT ellipse emmeans estimability evaluate factoextra FactoMineR fansi farver fastmap flashClust fontawesome foreach formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif glue gplots gridExtra gtable gtools highcharter highr htmltools htmlwidgets httpuv httr igraph impute IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval leaps lifecycle limma lme4 lubridate magrittr MALDIquant MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa modelr MsCoreUtils MSnbase multcompView MultiAssayExperiment munsell mvtnorm mzID mzR ncdf4 nlme nloptr nnet numDeriv openssl pbkrtest pcaMethods pillar pkgconfig plotly plyr polynom preprocessCore promises ProtGenerics PSMatch purrr QFeatures quantmod quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 Rhdf5lib rjson rlang rlist rmarkdown rstatix S4Arrays S4Vectors sass scales scatterplot3d shiny shinyBS shinyjqui shinyjs sm snow sourcetools SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange tinytex TTR UCSC.utils utf8 vctrs vioplot viridis viridisLite visNetwork vsn withr xfun XML xtable xts XVector yaml zlibbioc zoo

Adding third party plots

Samuel Wieczorek, Thomas Burger

Rendered fromaddingThirdPartyPlots.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-04-13
Started: 2024-03-11

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

Samuel Wieczorek, Thomas Burger

Rendered fromomXplore.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-04-13
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_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