Package: exploreDE 0.99.0

Witold Wolski

exploreDE: Interactive Exploration of Differential Expression Results

A Shiny application to help users explore and enjoy their 'omics data, and make publication-quality figures. It shows differential expression results from RNA-seq, proteomics and CRISPR screens as ordination plots, heatmaps, volcano plots, box plots, GO and KEGG pathway views, and ORA and GSEA tables. The app reads AnnData ('.h5ad') files in the exploreDE/1.0 layout, which build_explore_h5ad() writes from counts, sample tables, DE tables and enrichment results, and the SummarizedExperiment results of the FGCZ SUSHI and prolfqua pipelines. App settings are saved and restored as JSON session files.

Authors:Peter Leary [aut], Witold Wolski [cre], Functional Genomics Center Zurich [fnd]

exploreDE_0.99.0.tar.gz
exploreDE_0.99.0.tgz(r-4.6-any)exploreDE_0.99.0.tgz(r-4.5-any)
exploreDE_0.99.0.tar.gz(r-4.7-any)exploreDE_0.99.0.tar.gz(r-4.6-any)
exploreDE_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
exploreDE/json (API)

# Install 'exploreDE' in R:
install.packages('exploreDE', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fgcz/explorede/issues

Pkgdown/docs site:https://fgcz.github.io

On CRAN:

Conda:

softwareshinyappsguivisualizationdifferentialexpressiongeneexpressionrnaseqtranscriptomicsproteomicscrisprgenesetenrichmentpathwaysgokegg

4.94 score 11 exports 265 dependencies

Last updated from:0a0839713a. Checks:1 NOTE, 6 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE284
linux-develOK625
source / vignettesOK336
linux-releaseOK738
macos-releaseOK674
macos-oldrelOK674
windows-develFAIL2245
windows-releaseFAIL1993
windows-oldrelFAIL2013
wasm-releaseOK265

Exports:build_explore_h5adExploreDatasetExploreDatasetH5ADExploreDatasetSEExploreDatasetSE_CountQCExploreDatasetSE_CrisprCountQCExploreDatasetSE_ProteomicsExploreDatasetSE_RNASeqexploreDEnew_explore_datasetvalidate_explore_dataset

Dependencies:abindaisdkanndataRAnnotationDbiapeaplotaskpassassertthatassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocParallelBiostringsbitbit64blobbootbroombslibcachemcallrcarcarDatacharportcheckmatecirclizeclicliprclueclusterclusterProfilercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydendextendDerivDESeq2digestdir.expirydoBydoParallelDOSEdplyrDTenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachforecastformatRFormulafracdifffreshfsfutile.loggerfutile.optionsgdtoolsgenericsGenomicRangesGetoptLongGGallyggbeeswarmggforceggfunggiraphggnewscaleggplot2ggplotifyggprismggpubrggrepelggsciggsignifggstatsggtangleggtreeggvennGlobalOptionsglueGO.dbGOSemSimgridExtragridGraphicsgsongtablegtoolsherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonlitekableExtraKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallearnrlifecyclelimmalitedownlme4lmtestlocfitmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimeminiUIminqamodelrnlmenloptrnnetnumDerivofficeropensslopenxlsxotelpatchworkpbkrtestpermutepillarpkgconfigplotlyplyrpngpolyclippolynomprettyunitsprocessxprogresspromisespspurrrqs2quantregqvalueR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppTOMLRdpackreadrreformulasrenvreshape2reticulaterhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownrprojrootRSQLiterstatixrstudioapiS4ArraysS4VectorsS7sassscalesscatterpiescuttleSeqinfoshapeshinyshinycssloadersshinydashboardshinyjsSingleCellExperimentsnowsortablesourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsvglitesyssystemfontstextshapingtibbletidydrtidyrtidyselecttidytreetimeDatetinytextreeiotreelayouttweenrtzdburcautf8uuidvctrsveganviporviridisviridisLitevroomwaiterwithrxfunxml2xtableXVectoryamlyulab.utilszipzoo

Bring your own data: building an exploreDE file
Install and run | What goes into a file | Counts only | Proteomics with one contrast | RNA-seq with DE and pathways | Check the file before you open it | How columns are recognised | When a column isn't recognised | Feature level | Organisms without an annotation package | Writing the file outside R | Opening a file from a link | Saving your settings | Session info
Rendered frombring-your-own-data.Rmdusingknitr::rmarkdown

Last update: 2026-11-14
Started: 2026-09-25

exploreDE: interactive exploration of differential expression results
Overview | exploreDE and Bioconductor | Installation | Starting the app | A tour of the app | Datasets in R | Your own data | Getting help | Session info
Rendered fromexploreDE.Rmdusingknitr::rmarkdown

Last update: 2026-11-14
Started: 2026-11-14