Package: exploreDE
Type: Package
Title: Interactive Exploration of Differential Expression Results
Version: 0.99.0
Authors@R: c(
  person("Peter", "Leary", email = "peter.leary@uzh.ch", role = "aut",
         comment = c(ORCID = "0000-0003-1430-6185")),
  person("Witold", "Wolski", email = "wewolski@gmail.com", role = "cre",
         comment = c(ORCID = "0000-0002-6468-120X")),
  person("Functional Genomics Center Zurich", role = "fnd"))
Description: 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.
License: MIT + file LICENSE
URL: https://fgcz.github.io/exploreDE/,
        https://github.com/fgcz/exploreDE
BugReports: https://github.com/fgcz/exploreDE/issues
biocViews: Software, ShinyApps, GUI, Visualization,
        DifferentialExpression, GeneExpression, RNASeq,
        Transcriptomics, Proteomics, CRISPR, GeneSetEnrichment,
        Pathways, GO, KEGG
Encoding: UTF-8
Depends: R (>= 4.5.0)
Imports: shiny, shinydashboard, ggpubr, plotly, DESeq2, RColorBrewer,
        ComplexHeatmap, clusterProfiler, DT, colourpicker, circlize,
        kableExtra, ggrepel, sortable, waiter, ggprism, ggbeeswarm,
        rstatix, parallel, shinyjs, shinycssloaders, GGally, Matrix,
        fresh, scuttle, qs2, vegan, limma, officer, R6, anndataR (>=
        1.2.3), rhdf5, jsonlite, curl, SummarizedExperiment, S4Vectors,
        dplyr, ggplot2, gtools, matrixStats, methods, openxlsx, readr,
        tibble, xml2, dendextend, rlang, colorspace, cowplot,
        enrichplot, ggvenn, scales, tidyr, stats, utils, grDevices,
        graphics
Suggests: BiocManager, png, ggtext, gridtext, glmpca, pathview,
        KEGGREST, DOSE, testthat (>= 3.0.0), shinytest2, callr,
        jsonvalidate, systemfonts, ragg, nanoparquet, arrow, knitr,
        rmarkdown, BiocStyle, withr, devtools
VignetteBuilder: knitr
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.1
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev libglpk-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev perl python3 libx11-dev zlib1g-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-11-14 18:03:32 UTC
RemoteUrl: https://github.com/BiocStaging/exploreDE
RemoteRef: HEAD
RemoteSha: 0a0839713a11b83aecac2e7b0cc3bbc4543f1398
NeedsCompilation: no
Packaged: 2026-11-14 18:58:10 UTC; root
Author: Peter Leary [aut] (ORCID: <https://orcid.org/0000-0003-1430-6185>),
  Witold Wolski [cre] (ORCID: <https://orcid.org/0000-0002-6468-120X>),
  Functional Genomics Center Zurich [fnd]
Maintainer: Witold Wolski <wewolski@gmail.com>