{ "_id": "6a6486c2d7a87e95b9704531", "Package": "debrowser", "Type": "Package", "Title": "Interactive Differential Expresion Analysis Browser", "Version": "1.41.2", "Date": "2026-07-23", "Authors@R": "c(\nperson(\"Alper\", \"Kucukural\",\nemail = \"alper.kucukural@umassmed.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Onur\", \"Yukselen\",\nemail = \"onur.yukselen@umassmed.edu\",\nrole = \"aut\"),\nperson(\"Manuel\", \"Garber\",\nemail = \"manuel.garber@umassmed.edu\",\nrole = \"aut\"))", "Description": "Bioinformatics platform containing interactive plots and\ntables for differential gene and region expression studies.\nAllows visualizing expression data much more deeply in an\ninteractive and faster way. By changing the parameters, users\ncan easily discover different parts of the data that like never\nhave been done before. Manually creating and looking these\nplots takes time. With DEBrowser users can prepare plots\nwithout writing any code. Differential expression, PCA and\nclustering analysis are made on site and the results are shown\nin various plots such as scatter, bar, box, volcano, ma plots\nand Heatmaps.", "License": "GPL-3 + file LICENSE", "RoxygenNote": "8.0.0", "Encoding": "UTF-8", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/UMMS-Biocore/debrowser,\nhttps://debrowser.readthedocs.io", "BugReports": "https://github.com/UMMS-Biocore/debrowser/issues/new", "biocViews": "Sequencing, ChIPSeq, RNASeq, DifferentialExpression,\nGeneExpression, Clustering, ImmunoOncology", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-23 18:20:13 UTC", "RemoteUrl": "https://github.com/bioc/debrowser", "RemoteRef": "HEAD", "RemoteSha": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-25 09:26:24 UTC", "User": "root" }, "Author": "Alper Kucukural [aut, cre],\nOnur Yukselen [aut],\nManuel Garber [aut]", "Maintainer": "Alper Kucukural ", "_user": "bioc", "_type": "src", "_file": "debrowser_1.41.2.tar.gz", "_fileid": "https://r2.ropensci.org/59ef3694dd96709774f17c8ed378c31aeeddeb2ad859cf8f311907f7782e6579", "_filesize": 1941646, "_sha256": "59ef3694dd96709774f17c8ed378c31aeeddeb2ad859cf8f311907f7782e6579", "_expires": "2026-11-02T09:49:52.000Z", "_created": "2026-07-25T09:26:24.000Z", "_published": "2026-07-25T09:49:54.453Z", "_jobs": [ { "job": 89665988264, "time": 283, "config": "bioc-checks", "r": "4.6.1", "check": "FAILURE", "artifact": "" }, { "job": 89665988279, "time": 740, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8618271407" }, { "job": 89665988284, "time": 673, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8618262827" }, { "job": 89665988275, "time": 332, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8618181208" }, { "job": 89665988298, "time": 376, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8618187064" }, { "job": 89665470687, "time": 460, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8618140823" }, { "job": 89665988292, "time": 270, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8618212159" }, { "job": 89665988303, "time": 481, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8618242428" }, { "job": 89665988301, "time": 516, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8618244398" }, { "job": 89665988295, "time": 504, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8618241938" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395", "_status": "success", "_upstream": "https://github.com/bioc/debrowser", "_commit": { "id": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "author": "Alper Kucukural ", "committer": "Alper Kucukural ", "message": "fix(bioc): drop sodium dep (breaks nebbiolo2 check); use scrypt+openssl\n\nsodium is absent on the Bioconductor Linux builder (nebbiolo2 has no\nlibsodium), so R CMD check failed there at the dependency stage with\n\"Package suggested but not available: 'sodium'\" before any other check\nran, blocking propagation of the package. scrypt and openssl are both\nalready Imports of shinymanager and present on every Bioc builder.\n\n- Password hashing: libsodium argon2id -> scrypt::hashPassword(), the\n same primitive shinymanager stores. verify_password() tolerates a\n malformed stored hash (failed login, not an error).\n- Per-user AI key encryption: libsodium secretbox -> AES-256-GCM.\n openssl's aes_gcm_* neither emits nor verifies a GCM tag, so\n authenticate explicitly with encrypt-then-MAC (HMAC-SHA256); enc/mac\n subkeys are domain-separated via derive_user_key(purpose=). Blob\n layout is now iv(12) || ciphertext || hmac(32), verified with a\n non-short-circuiting compare before decrypt.\n- Regression guard test-deps-no-sodium.R fails if sodium reappears.\n- Docs (signup, Rd, privacy.html) updated off argon2id.\n- Bump 1.41.1 -> 1.41.2 so Bioc picks up the fix; NEWS documents the\n crypto swap and that pre-1.41.2 hashes/keys are not readable.\n\nCo-Authored-By: Claude Opus 4.8 (1M context) \n", "time": 1784830813 }, "_maintainer": { "name": "Alper Kucukural", "email": "alper.kucukural@umassmed.edu", "login": "nephantes", "description": "", "uuid": 4869692 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "shiny", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "shinyBS", "role": "Imports" }, { "package": "shinyWidgets", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "annotate", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "clusterProfiler", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "RCurl", "role": "Imports" }, { "package": "colourpicker", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "heatmaply", "role": "Imports" }, { "package": "bslib", "version": ">= 0.7.0", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "testthat", "version": ">= 3.2.0", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RSQLite", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "shinymanager", "version": ">= 1.0.4", "role": "Suggests" }, { "package": "shinytest2", "role": "Suggests" }, { "package": "chromote", "role": "Suggests" }, { "package": "DBI", "role": "Suggests" }, { "package": "Harman", "role": "Suggests" }, { "package": "pathview", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "apeglm", "role": "Suggests" }, { "package": "ashr", "role": "Suggests" }, { "package": "commonmark", "role": "Suggests" }, { "package": "enrichplot", "role": "Suggests" }, { "package": "fgsea", "role": "Suggests" }, { "package": "ipaddress", "version": ">= 1.0", "role": "Suggests" }, { "package": "mockery", "role": "Suggests" }, { "package": "msigdbr", "role": "Suggests" }, { "package": "openssl", "role": "Suggests" }, { "package": "scrypt", "role": "Suggests" }, { "package": "UpSetR", "role": "Suggests" }, { "package": "DOSE", "role": "Suggests" }, { "package": "ellmer", "version": ">= 0.1.0", "role": "Suggests" }, { "package": "keyring", "role": "Suggests" }, { "package": "whisker", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "xml2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-30", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "chipseq", "rnaseq", "differentialexpression", "geneexpression", "clustering", "immunooncology" ], "_stars": 62, "_contributors": [ { "user": "nephantes", "count": 249, "uuid": 4869692 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "onuryukselen", "count": 6, "uuid": 33356633 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "dtenenba", "count": 4, "uuid": 2286826 }, { "user": "artur-man", "count": 2, "uuid": 39335576 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 451, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_devurl": "https://github.com/umms-biocore/debrowser", "_searchresults": 141, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/debrowser.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/umms-biocore/debrowser", "_realowner": "bioc", "_cranurl": false, "_exports": [ "accountDropdownServer", "accountDropdownUI", "actionButtonDE", "addDataCols", "addID", "ai_chat", "ai_interpret", "aiInterpretServer", "aiInterpretUI", "aiSettingsServer", "aiSettingsUI", "all2all", "all2allControlsUI", "apply_batch_correction", "apply_de_filters", "apply_merged_filters", "applyFilters", "applyFiltersNew", "applyFiltersToMergedComparison", "barMainPlotControlsUI", "batchEffectUI", "batchMethod", "BoxMainPlotControlsUI", "changeClusterOrder", "checkCountData", "checkMetaData", "clusterData", "clustFunParamsUI", "compareClust", "comparison_labels", "comparisonConcordanceServer", "comparisonConcordanceUI", "compute_pill_class", "concordance_sets", "concordance_summary", "condSelectServer", "condSelectUI", "cooks_outlier_summary", "correctCombat", "correctHarman", "create_debrowser_user", "customColorsUI", "cutoff_presets", "cutOffSelectionServer", "cutOffSelectionUI", "dataLCFUI", "dataLoadUI", "de_assert_count_matrix", "de_card", "de_direction_summary", "de_error", "de_eyebrow", "de_headline", "de_nav_chip", "de_progress_label", "de_stat", "de_stat_strip", "de_style_guide", "de_theme", "de_workbar", "debrowserall2all", "debrowserbarmainplot", "debrowserbatcheffect", "debrowserboxmainplot", "debrowserdataload", "debrowserdeanalysis", "debrowserdensityplot", "debrowserheatmap", "debrowserhistogram", "debrowserIQRplot", "debrowserlowcountfilter", "debrowsermainplot", "debrowserpcaplot", "debrowserqccooks", "debrowserqcdetectionrate", "debrowserqcdispersion", "debrowserqclibrarydepth", "debrowserqcmtpct", "debrowserqcsampledist", "debrowserqcsizefactors", "default_cutoffs", "dendControlsUI", "densityPlotControlsUI", "deServer", "detect_separator", "detection_rate", "deUI", "distFunParamsUI", "drawKEGG", "drawPCAExplained", "enrichmentGmtServer", "enrichmentGmtUI", "enrichmentNesHeatmapServer", "enrichmentNesHeatmapUI", "enrichmentServer", "enrichmentUI", "exportMenuItems", "exportMenuServer", "exportMenuUI", "fileTypes", "fileUploadBox", "filter_low_counts", "filter_params_from_input", "flag_outliers_2sd", "fold_to_log2fc", "generateTestData", "get_most_varied", "get_table_data", "getAfterLoadMsg", "getAll2AllPlotUI", "getBarMainPlot", "getBarMainPlotUI", "getBoxMainPlot", "getBoxMainPlotUI", "getBSTableUI", "getColors", "getColorShapeSelection", "getCompSelection", "getCondMsg", "getCutOffSelection", "getDataAssesmentText", "getDataForTables", "getDataPreparationText", "getDEAnalysisText", "getDensityPlot", "getDensityPlotUI", "getDEResultsUI", "getDomains", "getDown", "getDownloadSection", "getEnrichDO", "getEnrichGO", "getEnrichKEGG", "getEntrezIds", "getEntrezTable", "getGeneList", "getGeneSetData", "getGOLeftMenu", "getGoPanel", "getGOPlots", "getGSEA", "getHeatmapUI", "getHelpButton", "getHideLegendOnOff", "getHistogramUI", "getIntroText", "getIQRPlot", "getIQRPlotUI", "getJSLine", "getKEGGModal", "getLeftMenu", "getLegendColors", "getLegendRadio", "getLegendSelect", "getLevelOrder", "getLogo", "getMainPanel", "getMainPlotsLeftMenu", "getMainPlotUI", "getMean", "getMergedComparison", "getMostVariedList", "getNormalizedMatrix", "getOrganism", "getOrganismBox", "getOrganismPathway", "getPCAcontolUpdatesJS", "getPCAexplained", "getPCAPlotUI", "getPCselection", "getPlotArea", "getProgramTitle", "getQAText", "getQCLeftMenu", "getQCPanel", "getSampleDetails", "getSearchData", "getSelectedCols", "getSelectedDatasetInput", "getSelHeat", "getShapeColor", "getStartPlotsMsg", "getStartupMsg", "getTableDetails", "getTableModal", "getTableStyle", "getTabUpdateJS", "getUp", "getUpDown", "getVariationData", "gmt_to_pathways", "heatmapControlsUI", "heatmapJScode", "heatmapServer", "heatmapUI", "hideObj", "histogramControlsUI", "install_cutoff_preset_observers", "IQRPlotControlsUI", "kmeansControlsUI", "lcfMetRadio", "library_depth_summary", "list_models", "log2fc_to_fold", "mainPlotControlsUI", "mainScatterNew", "make_default_metadata", "match_preset", "merge_comparisons", "methods_paragraph", "msigdb_pathways", "mt_pct_per_sample", "nes_heatmap_data", "niceKmeans", "normalizationMethods", "normalize_counts", "palUI", "panel.cor", "panel.hist", "pcaPlotControlsUI", "plot_de_direction_bar", "plot_de_pairwise_heatmap", "plot_method_scatter", "plot_method_upset", "plot_pca", "plotData", "plotMarginsUI", "plotSizeMarginsUI", "plotSizeUI", "plotTypeUI", "prepDataContainer", "prepGroup", "prepHeatData", "prepPCADat", "progress_message", "push", "qc_keep_cols", "qc_keep_meta_rows", "qcCooksUI", "qcDetectionRateUI", "qcDispersionUI", "qcLibraryDepthUI", "qcMtPctUI", "qcSampleDistUI", "qcSizeFactorsUI", "removeCols", "removeExtraCols", "require_pkg", "resend_verification_email", "reset_debrowser_password", "round_vals", "run_de", "run_de_methods", "run_deseq2", "run_edger", "run_gsea", "run_limma", "run_pca", "runDE", "runDESeq2", "runEdgeR", "runHeatmap", "runHeatmap2", "runLimma", "sample_distance_matrix", "search_geneset", "select_dataset", "selectGroupInfo", "sepRadio", "setBatch", "showObj", "size_factor_library_summary", "startDEBrowser", "startHeatmap", "textareaInput", "togglePanels", "update_progress" ], "_help": [ { "page": "accountDropdownServer", "title": "Server: wires the dropdown to current_user, signup modal, signout.", "topics": [ "accountDropdownServer" ] }, { "page": "accountDropdownUI", "title": "UI: navbar account dropdown.", "topics": [ "accountDropdownUI" ] }, { "page": "actionButtonDE", "title": "Buttons including Action Buttons and Event Buttons", "topics": [ "actionButtonDE" ] }, { "page": "addDataCols", "title": "addDataCols", "topics": [ "addDataCols" ] }, { "page": "addID", "title": "addID", "topics": [ "addID" ] }, { "page": "ai_chat", "title": "Build an ellmer chat object for the configured provider/model.", "topics": [ "ai_chat" ] }, { "page": "ai_interpret", "title": "Send a redacted analytical question to a configured LLM provider.", "topics": [ "ai_interpret" ] }, { "page": "aiInterpretServer", "title": "AI interpretation panel server.", "topics": [ "aiInterpretServer" ] }, { "page": "aiInterpretUI", "title": "AI interpretation panel UI.", "topics": [ "aiInterpretUI" ] }, { "page": "aiSettingsServer", "title": "Settings server - opens the AI configuration modal on click.", "topics": [ "aiSettingsServer" ] }, { "page": "aiSettingsUI", "title": "Settings nav_menu UI (mounted in the navbar).", "topics": [ "aiSettingsUI" ] }, { "page": "all2all", "title": "all2all", "topics": [ "all2all" ] }, { "page": "all2allControlsUI", "title": "all2allControlsUI", "topics": [ "all2allControlsUI" ] }, { "page": "apply_batch_correction", "title": "Apply batch-effect correction.", "topics": [ "apply_batch_correction" ] }, { "page": "apply_de_filters", "title": "Apply DE filters and label Up/Down/NS/MV/GS rows.", "topics": [ "apply_de_filters" ] }, { "page": "apply_merged_filters", "title": "Apply Up/Down cutoffs across a merged-comparisons table.", "topics": [ "apply_merged_filters" ] }, { "page": "applyFilters", "title": "applyFilters", "topics": [ "applyFilters" ] }, { "page": "applyFiltersNew", "title": "applyFiltersNew", "topics": [ "applyFiltersNew" ] }, { "page": "applyFiltersToMergedComparison", "title": "applyFiltersToMergedComparison", "topics": [ "applyFiltersToMergedComparison" ] }, { "page": "barMainPlotControlsUI", "title": "barMainPlotControlsUI", "topics": [ "barMainPlotControlsUI" ] }, { "page": "batchEffectUI", "title": "batchEffectUI Creates a panel to coorect batch effect", "topics": [ "batchEffectUI" ] }, { "page": "batchMethod", "title": "batchMethod", "topics": [ "batchMethod" ] }, { "page": "BoxMainPlotControlsUI", "title": "BoxMainPlotControlsUI", "topics": [ "BoxMainPlotControlsUI" ] }, { "page": "changeClusterOrder", "title": "changeClusterOrder", "topics": [ "changeClusterOrder" ] }, { "page": "checkCountData", "title": "checkCountData", "topics": [ "checkCountData" ] }, { "page": "checkMetaData", "title": "checkMetaData", "topics": [ "checkMetaData" ] }, { "page": "clusterData", "title": "clusterData", "topics": [ "clusterData" ] }, { "page": "clustFunParamsUI", "title": "clustFunParamsUI", "topics": [ "clustFunParamsUI" ] }, { "page": "compareClust", "title": "compareClust", "topics": [ "compareClust" ] }, { "page": "comparison_labels", "title": "Build unique display labels for a list of comparisons.", "topics": [ "comparison_labels" ] }, { "page": "comparisonConcordanceServer", "title": "Server for the Comparison Concordance tab.", "topics": [ "comparisonConcordanceServer" ] }, { "page": "comparisonConcordanceUI", "title": "UI for the Comparison Concordance top-level tab.", "topics": [ "comparisonConcordanceUI" ] }, { "page": "compute_pill_class", "title": "Compute the CSS class name for a pill given its progress state.", "topics": [ "compute_pill_class" ] }, { "page": "concordance_sets", "title": "Build per-method significant-gene sets.", "topics": [ "concordance_sets" ] }, { "page": "concordance_summary", "title": "Pairwise concordance summary across DE methods.", "topics": [ "concordance_summary" ] }, { "page": "condSelectServer", "title": "Comparison-Selection wizard server.", "topics": [ "condSelectServer" ] }, { "page": "condSelectUI", "title": "Comparison-Selection wizard UI.", "topics": [ "condSelectUI" ] }, { "page": "cooks_outlier_summary", "title": "Per-sample Cook's distance outlier counts.", "topics": [ "cooks_outlier_summary" ] }, { "page": "correctCombat", "title": "Correct Batch Effect using Combat in sva package", "topics": [ "correctCombat" ] }, { "page": "correctHarman", "title": "Correct Batch Effect using Harman", "topics": [ "correctHarman" ] }, { "page": "create_debrowser_user", "title": "Create a debrowser user from the R console.", "topics": [ "create_debrowser_user" ] }, { "page": "customColorsUI", "title": "customColorsUI", "topics": [ "customColorsUI" ] }, { "page": "cutoff_presets", "title": "Cutoff preset table.", "topics": [ "cutoff_presets" ] }, { "page": "cutOffSelectionServer", "title": "cutOffSelectionServer", "topics": [ "cutOffSelectionServer" ] }, { "page": "cutOffSelectionUI", "title": "cutOffSelectionUI", "topics": [ "cutOffSelectionUI" ] }, { "page": "dataLCFUI", "title": "dataLCFUI Creates a panel to filter low count genes and regions", "topics": [ "dataLCFUI" ] }, { "page": "dataLoadUI", "title": "dataLoadUI", "topics": [ "dataLoadUI" ] }, { "page": "de_assert_count_matrix", "title": "Validate that x is a non-empty numeric count matrix.", "topics": [ "de_assert_count_matrix" ] }, { "page": "de_card", "title": "de_card", "topics": [ "de_card" ] }, { "page": "de_direction_summary", "title": "Per-entry up / down / total significant gene counts.", "topics": [ "de_direction_summary" ] }, { "page": "de_error", "title": "Raise a structured DEBrowser error.", "topics": [ "de_error" ] }, { "page": "de_eyebrow", "title": "de_eyebrow", "topics": [ "de_eyebrow" ] }, { "page": "de_headline", "title": "de_headline", "topics": [ "de_headline" ] }, { "page": "de_nav_chip", "title": "de_nav_chip", "topics": [ "de_nav_chip" ] }, { "page": "de_progress_label", "title": "Render a label suitable for nav_panel(title=) or actionLink(label=) that includes a slot the JS handler can decorate with a progress icon.", "topics": [ "de_progress_label" ] }, { "page": "de_stat", "title": "de_stat", "topics": [ "de_stat" ] }, { "page": "de_stat_strip", "title": "de_stat_strip", "topics": [ "de_stat_strip" ] }, { "page": "de_style_guide", "title": "Open the DEBrowser design-system style guide", "topics": [ "de_style_guide" ] }, { "page": "de_theme", "title": "de_theme", "topics": [ "de_theme" ] }, { "page": "de_workbar", "title": "de_workbar", "topics": [ "de_workbar" ] }, { "page": "debrowserall2all", "title": "debrowserall2all", "topics": [ "debrowserall2all" ] }, { "page": "debrowserbarmainplot", "title": "debrowserbarmainplot", "topics": [ "debrowserbarmainplot" ] }, { "page": "debrowserbatcheffect", "title": "debrowserbatcheffect", "topics": [ "debrowserbatcheffect" ] }, { "page": "debrowserboxmainplot", "title": "debrowserboxmainplot", "topics": [ "debrowserboxmainplot" ] }, { "page": "debrowserdataload", "title": "debrowserdataload", "topics": [ "debrowserdataload" ] }, { "page": "debrowserdeanalysis", "title": "debrowserdeanalysis", "topics": [ "debrowserdeanalysis" ] }, { "page": "debrowserdensityplot", "title": "debrowserdensityplot", "topics": [ "debrowserdensityplot" ] }, { "page": "debrowserheatmap", "title": "debrowserheatmap", "topics": [ "debrowserheatmap" ] }, { "page": "debrowserhistogram", "title": "debrowserhistogram", "topics": [ "debrowserhistogram" ] }, { "page": "debrowserIQRplot", "title": "debrowserIQRplot", "topics": [ "debrowserIQRplot" ] }, { "page": "debrowserlowcountfilter", "title": "debrowserlowcountfilter", "topics": [ "debrowserlowcountfilter" ] }, { "page": "debrowsermainplot", "title": "debrowsermainplot", "topics": [ "debrowsermainplot" ] }, { "page": "debrowserpcaplot", "title": "debrowserpcaplot", "topics": [ "debrowserpcaplot" ] }, { "page": "debrowserqccooks", "title": "debrowserqccooks", "topics": [ "debrowserqccooks" ] }, { "page": "debrowserqcdetectionrate", "title": "debrowserqcdetectionrate", "topics": [ "debrowserqcdetectionrate" ] }, { "page": "debrowserqcdispersion", "title": "debrowserqcdispersion", "topics": [ "debrowserqcdispersion" ] }, { "page": "debrowserqclibrarydepth", "title": "debrowserqclibrarydepth", "topics": [ "debrowserqclibrarydepth" ] }, { "page": "debrowserqcmtpct", "title": "debrowserqcmtpct", "topics": [ "debrowserqcmtpct" ] }, { "page": "debrowserqcsampledist", "title": "debrowserqcsampledist", "topics": [ "debrowserqcsampledist" ] }, { "page": "debrowserqcsizefactors", "title": "debrowserqcsizefactors", "topics": [ "debrowserqcsizefactors" ] }, { "page": "default_cutoffs", "title": "Default DE significance cutoffs.", "topics": [ "default_cutoffs" ] }, { "page": "dendControlsUI", "title": "dendControlsUI", "topics": [ "dendControlsUI" ] }, { "page": "densityPlotControlsUI", "title": "densityPlotControlsUI", "topics": [ "densityPlotControlsUI" ] }, { "page": "deServer", "title": "deServer", "topics": [ "deServer" ] }, { "page": "detect_separator", "title": "Auto-detect the field separator in a count-data file.", "topics": [ "detect_separator" ] }, { "page": "detection_rate", "title": "Per-sample gene detection rate.", "topics": [ "detection_rate" ] }, { "page": "deUI", "title": "deUI", "topics": [ "deUI" ] }, { "page": "distFunParamsUI", "title": "distFunParamsUI", "topics": [ "distFunParamsUI" ] }, { "page": "drawKEGG", "title": "drawKEGG", "topics": [ "drawKEGG" ] }, { "page": "drawPCAExplained", "title": "Creates a more detailed plot using the PCA results from the selected dataset.", "topics": [ "drawPCAExplained" ] }, { "page": "enrichmentGmtServer", "title": "Server for the gene-set source picker.", "topics": [ "enrichmentGmtServer" ] }, { "page": "enrichmentGmtUI", "title": "UI for the gene-set source picker (Enrichment tab sidebar).", "topics": [ "enrichmentGmtUI" ] }, { "page": "enrichmentNesHeatmapServer", "title": "Server for the NES heatmap card.", "topics": [ "enrichmentNesHeatmapServer" ] }, { "page": "enrichmentNesHeatmapUI", "title": "UI for the NES heatmap card.", "topics": [ "enrichmentNesHeatmapUI" ] }, { "page": "enrichmentServer", "title": "Server for the Enrichment tab.", "topics": [ "enrichmentServer" ] }, { "page": "enrichmentUI", "title": "UI for the Enrichment tab.", "topics": [ "enrichmentUI" ] }, { "page": "exportMenuItems", "title": "Export menu items (without nav_menu wrapper) for embedding in the account dropdown. Returns a list of `
  • `s, each carrying either a shiny-download-link (downloads) or a `data-debrowser-input` action link (modal opens). IDs are namespaced under `id` so the existing `exportMenuServer(id, ...)` observers/handlers wire up unchanged.", "topics": [ "exportMenuItems" ] }, { "page": "exportMenuServer", "title": "Export menu server - wires download handlers from a state reactive.", "topics": [ "exportMenuServer" ] }, { "page": "exportMenuUI", "title": "Export menu UI - navbar dropdown.", "topics": [ "exportMenuUI" ] }, { "page": "fileTypes", "title": "fileTypes", "topics": [ "fileTypes" ] }, { "page": "fileUploadBox", "title": "fileUploadBox", "topics": [ "fileUploadBox" ] }, { "page": "filter_low_counts", "title": "Filter low-count rows from a count matrix.", "topics": [ "filter_low_counts" ] }, { "page": "filter_params_from_input", "title": "Translate a Shiny `input` reactive into a structured filter-params list.", "topics": [ "filter_params_from_input" ] }, { "page": "flag_outliers_2sd", "title": "Flag values further than 2 standard deviations from the mean.", "topics": [ "flag_outliers_2sd" ] }, { "page": "fold_to_log2fc", "title": "Convert fold-change cutoff to |log2FC|.", "topics": [ "fold_to_log2fc" ] }, { "page": "generateTestData", "title": "generateTestData", "topics": [ "generateTestData" ] }, { "page": "get_most_varied", "title": "Compute the most-varied genes by coefficient of variation.", "topics": [ "get_most_varied" ] }, { "page": "get_table_data", "title": "Build the (data, padj_colname, fold_colname) tuple for the Tables tab.", "topics": [ "get_table_data" ] }, { "page": "getAfterLoadMsg", "title": "getAfterLoadMsg", "topics": [ "getAfterLoadMsg" ] }, { "page": "getAll2AllPlotUI", "title": "getAll2AllPlotUI", "topics": [ "getAll2AllPlotUI" ] }, { "page": "getBarMainPlot", "title": "getBarMainPlot", "topics": [ "getBarMainPlot" ] }, { "page": "getBarMainPlotUI", "title": "getBarMainPlotUI", "topics": [ "getBarMainPlotUI" ] }, { "page": "getBoxMainPlot", "title": "getBoxMainPlot", "topics": [ "getBoxMainPlot" ] }, { "page": "getBoxMainPlotUI", "title": "getBoxMainPlotUI", "topics": [ "getBoxMainPlotUI" ] }, { "page": "getBSTableUI", "title": "getBSTableUI prepares a Modal to put a table", "topics": [ "getBSTableUI" ] }, { "page": "getColors", "title": "getColors", "topics": [ "getColors" ] }, { "page": "getColorShapeSelection", "title": "getColorShapeSelection", "topics": [ "getColorShapeSelection" ] }, { "page": "getCompSelection", "title": "getCompSelection", "topics": [ "getCompSelection" ] }, { "page": "getCondMsg", "title": "getCondMsg", "topics": [ "getCondMsg" ] }, { "page": "getCutOffSelection", "title": "getCutOffSelection", "topics": [ "getCutOffSelection" ] }, { "page": "getDataAssesmentText", "title": "getDataAssesmentText DataAssesment text", "topics": [ "getDataAssesmentText" ] }, { "page": "getDataForTables", "title": "getDataForTables get data to fill up tables tab", "topics": [ "getDataForTables" ] }, { "page": "getDataPreparationText", "title": "getDataPreparationText DataPreparation text", "topics": [ "getDataPreparationText" ] }, { "page": "getDEAnalysisText", "title": "getDEAnalysisText DEAnalysis text", "topics": [ "getDEAnalysisText" ] }, { "page": "getDensityPlot", "title": "getDensityPlot", "topics": [ "getDensityPlot" ] }, { "page": "getDensityPlotUI", "title": "getDensityPlotUI", "topics": [ "getDensityPlotUI" ] }, { "page": "getDEResultsUI", "title": "getDEResultsUI Creates a panel to visualize DE results", "topics": [ "getDEResultsUI" ] }, { "page": "getDomains", "title": "getDomains", "topics": [ "getDomains" ] }, { "page": "getDown", "title": "getDown get down regulated data", "topics": [ "getDown" ] }, { "page": "getDownloadSection", "title": "getDownloadSection", "topics": [ "getDownloadSection" ] }, { "page": "getEnrichDO", "title": "getEnrichDO", "topics": [ "getEnrichDO" ] }, { "page": "getEnrichGO", "title": "getEnrichGO", "topics": [ "getEnrichGO" ] }, { "page": "getEnrichKEGG", "title": "getEnrichKEGG", "topics": [ "getEnrichKEGG" ] }, { "page": "getEntrezIds", "title": "getEntrezIds", "topics": [ "getEntrezIds" ] }, { "page": "getEntrezTable", "title": "getEntrezTable", "topics": [ "getEntrezTable" ] }, { "page": "getGeneList", "title": "getGeneList", "topics": [ "getGeneList" ] }, { "page": "getGeneSetData", "title": "getGeneSetData", "topics": [ "getGeneSetData" ] }, { "page": "getGOLeftMenu", "title": "getGOLeftMenu", "topics": [ "getGOLeftMenu" ] }, { "page": "getGoPanel", "title": "getGoPanel", "topics": [ "getGoPanel" ] }, { "page": "getGOPlots", "title": "getGOPlots", "topics": [ "getGOPlots" ] }, { "page": "getGSEA", "title": "getGSEA", "topics": [ "getGSEA" ] }, { "page": "getHeatmapUI", "title": "getHeatmapUI", "topics": [ "getHeatmapUI" ] }, { "page": "getHelpButton", "title": "getHelpButton prepares a helpbutton for to go to a specific site in the documentation", "topics": [ "getHelpButton" ] }, { "page": "getHideLegendOnOff", "title": "getHideLegendOnOff", "topics": [ "getHideLegendOnOff" ] }, { "page": "getHistogramUI", "title": "getHistogramUI", "topics": [ "getHistogramUI" ] }, { "page": "getIntroText", "title": "getIntroText Intro text", "topics": [ "getIntroText" ] }, { "page": "getIQRPlot", "title": "getIQRPlot", "topics": [ "getIQRPlot" ] }, { "page": "getIQRPlotUI", "title": "getIQRPlotUI", "topics": [ "getIQRPlotUI" ] }, { "page": "getJSLine", "title": "getJSLine", "topics": [ "getJSLine" ] }, { "page": "getKEGGModal", "title": "getKEGGModal prepares a modal for KEGG plots", "topics": [ "getKEGGModal" ] }, { "page": "getLeftMenu", "title": "getLeftMenu", "topics": [ "getLeftMenu" ] }, { "page": "getLegendColors", "title": "getLegendColors", "topics": [ "getLegendColors" ] }, { "page": "getLegendRadio", "title": "getLegendRadio", "topics": [ "getLegendRadio" ] }, { "page": "getLegendSelect", "title": "getLegendSelect", "topics": [ "getLegendSelect" ] }, { "page": "getLevelOrder", "title": "getLevelOrder", "topics": [ "getLevelOrder" ] }, { "page": "getLogo", "title": "getLogo", "topics": [ "getLogo" ] }, { "page": "getMainPanel", "title": "getMainPanel", "topics": [ "getMainPanel" ] }, { "page": "getMainPlotsLeftMenu", "title": "getMainPlotsLeftMenu", "topics": [ "getMainPlotsLeftMenu" ] }, { "page": "getMainPlotUI", "title": "getMainPlotUI", "topics": [ "getMainPlotUI" ] }, { "page": "getMean", "title": "getMean", "topics": [ "getMean" ] }, { "page": "getMergedComparison", "title": "getMergedComparison", "topics": [ "getMergedComparison" ] }, { "page": "getMostVariedList", "title": "getMostVariedList", "topics": [ "getMostVariedList" ] }, { "page": "getNormalizedMatrix", "title": "getNormalizedMatrix", "topics": [ "getNormalizedMatrix" ] }, { "page": "getOrganism", "title": "getOrganism", "topics": [ "getOrganism" ] }, { "page": "getOrganismBox", "title": "getOrganismBox", "topics": [ "getOrganismBox" ] }, { "page": "getOrganismPathway", "title": "getOrganismPathway", "topics": [ "getOrganismPathway" ] }, { "page": "getPCAcontolUpdatesJS", "title": "getPCAcontolUpdatesJS in the prep menu we have two PCA plots to show how batch effect correction worked. One set of PCA input controls updates two PCA plots with this JS.", "topics": [ "getPCAcontolUpdatesJS" ] }, { "page": "getPCAexplained", "title": "getPCAexplained", "topics": [ "getPCAexplained" ] }, { "page": "getPCAPlotUI", "title": "getPCAPlotUI", "topics": [ "getPCAPlotUI" ] }, { "page": "getPCselection", "title": "getPCselection", "topics": [ "getPCselection" ] }, { "page": "getPlotArea", "title": "getPlotArea", "topics": [ "getPlotArea" ] }, { "page": "getProgramTitle", "title": "getProgramTitle", "topics": [ "getProgramTitle" ] }, { "page": "getQAText", "title": "getQAText Some questions and answers", "topics": [ "getQAText" ] }, { "page": "getQCLeftMenu", "title": "getQCLeftMenu", "topics": [ "getQCLeftMenu" ] }, { "page": "getQCPanel", "title": "getQCPanel", "topics": [ "getQCPanel" ] }, { "page": "getSampleDetails", "title": "getSampleDetails", "topics": [ "getSampleDetails" ] }, { "page": "getSearchData", "title": "getSearchData", "topics": [ "getSearchData" ] }, { "page": "getSelectedCols", "title": "getSelectedCols", "topics": [ "getSelectedCols" ] }, { "page": "getSelectedDatasetInput", "title": "getSelectedDatasetInput", "topics": [ "getSelectedDatasetInput" ] }, { "page": "getSelHeat", "title": "getSelHeat", "topics": [ "getSelHeat" ] }, { "page": "getShapeColor", "title": "getShapeColor", "topics": [ "getShapeColor" ] }, { "page": "getStartPlotsMsg", "title": "getStartPlotsMsg", "topics": [ "getStartPlotsMsg" ] }, { "page": "getStartupMsg", "title": "getStartupMsg", "topics": [ "getStartupMsg" ] }, { "page": "getTableDetails", "title": "getTableDetails", "topics": [ "getTableDetails" ] }, { "page": "getTableModal", "title": "getTableModal prepares table modal for KEGG", "topics": [ "getTableModal" ] }, { "page": "getTableStyle", "title": "getTableStyle", "topics": [ "getTableStyle" ] }, { "page": "getTabUpdateJS", "title": "getTabUpdateJS", "topics": [ "getTabUpdateJS" ] }, { "page": "getUp", "title": "getUp get up regulated data", "topics": [ "getUp" ] }, { "page": "getUpDown", "title": "getUpDown get up+down regulated data", "topics": [ "getUpDown" ] }, { "page": "getVariationData", "title": "getVariationData", "topics": [ "getVariationData" ] }, { "page": "gmt_to_pathways", "title": "Read a GMT file into a named list of gene-symbol vectors.", "topics": [ "gmt_to_pathways" ] }, { "page": "heatmapControlsUI", "title": "heatmapControlsUI", "topics": [ "heatmapControlsUI" ] }, { "page": "heatmapJScode", "title": "heatmapJScode", "topics": [ "heatmapJScode" ] }, { "page": "heatmapServer", "title": "heatmapServer", "topics": [ "heatmapServer" ] }, { "page": "heatmapUI", "title": "heatmapUI", "topics": [ "heatmapUI" ] }, { "page": "hideObj", "title": "hideObj", "topics": [ "hideObj" ] }, { "page": "histogramControlsUI", "title": "histogramControlsUI", "topics": [ "histogramControlsUI" ] }, { "page": "install_cutoff_preset_observers", "title": "Install Shiny observers that synchronise a preset-button input with the (padj, log2fc_cutoff) numeric inputs.", "topics": [ "install_cutoff_preset_observers" ] }, { "page": "IQRPlotControlsUI", "title": "IQRPlotControlsUI", "topics": [ "IQRPlotControlsUI" ] }, { "page": "kmeansControlsUI", "title": "kmeansControlsUI", "topics": [ "kmeansControlsUI" ] }, { "page": "lcfMetRadio", "title": "lcfMetRadio", "topics": [ "lcfMetRadio" ] }, { "page": "library_depth_summary", "title": "Per-sample library depth summary.", "topics": [ "library_depth_summary" ] }, { "page": "list_models", "title": "List available models for a configured LLM provider.", "topics": [ "list_models" ] }, { "page": "log2fc_to_fold", "title": "Convert |log2FC| cutoff to fold-change cutoff.", "topics": [ "log2fc_to_fold" ] }, { "page": "mainPlotControlsUI", "title": "mainPlotControlsUI", "topics": [ "mainPlotControlsUI" ] }, { "page": "mainScatterNew", "title": "mainScatterNew", "topics": [ "mainScatterNew" ] }, { "page": "make_default_metadata", "title": "Build a single-condition single-batch metadata data frame.", "topics": [ "make_default_metadata" ] }, { "page": "match_preset", "title": "Identify which preset a (padj, log2fc) pair matches.", "topics": [ "match_preset" ] }, { "page": "merge_comparisons", "title": "Merge per-comparison DE results into one wide table.", "topics": [ "merge_comparisons" ] }, { "page": "methods_paragraph", "title": "Manuscript-ready methods paragraph.", "topics": [ "methods_paragraph" ] }, { "page": "msigdb_pathways", "title": "Fetch MSigDB gene sets as a named list of gene-symbol vectors.", "topics": [ "msigdb_pathways" ] }, { "page": "mt_pct_per_sample", "title": "Per-sample mitochondrial-transcript percentage.", "topics": [ "mt_pct_per_sample" ] }, { "page": "nes_heatmap_data", "title": "Reshape per-comparison GSEA results for the NES heatmap.", "topics": [ "nes_heatmap_data" ] }, { "page": "niceKmeans", "title": "niceKmeans", "topics": [ "niceKmeans" ] }, { "page": "normalizationMethods", "title": "normalizationMethods", "topics": [ "normalizationMethods" ] }, { "page": "normalize_counts", "title": "Normalize a count matrix.", "topics": [ "normalize_counts" ] }, { "page": "palUI", "title": "palUI", "topics": [ "palUI" ] }, { "page": "panel.cor", "title": "panel.cor", "topics": [ "panel.cor" ] }, { "page": "panel.hist", "title": "panel.hist", "topics": [ "panel.hist" ] }, { "page": "pcaPlotControlsUI", "title": "pcaPlotControlsUI", "topics": [ "pcaPlotControlsUI" ] }, { "page": "plot_de_direction_bar", "title": "Horizontal bar plot of up / down DEG counts per comparison.", "topics": [ "plot_de_direction_bar" ] }, { "page": "plot_de_pairwise_heatmap", "title": "Symmetric pairwise heatmap of significant DEG counts between groups.", "topics": [ "plot_de_pairwise_heatmap" ] }, { "page": "plot_method_scatter", "title": "Pairwise log2FC scatter between two named entries of a DE list.", "topics": [ "plot_method_scatter" ] }, { "page": "plot_method_upset", "title": "UpSet plot of DE-gene overlap across methods.", "topics": [ "plot_method_upset" ] }, { "page": "plot_pca", "title": "plot_pca", "topics": [ "plot_pca" ] }, { "page": "plotData", "title": "plotData", "topics": [ "plotData" ] }, { "page": "plotMarginsUI", "title": "plotMarginsUI", "topics": [ "plotMarginsUI" ] }, { "page": "plotSizeMarginsUI", "title": "plotSizeMarginsUI", "topics": [ "plotSizeMarginsUI" ] }, { "page": "plotSizeUI", "title": "plotSizeUI", "topics": [ "plotSizeUI" ] }, { "page": "plotTypeUI", "title": "plotTypeUI", "topics": [ "plotTypeUI" ] }, { "page": "prepDataContainer", "title": "Run DE per comparison and return the downstream `dclist` payload.", "topics": [ "prepDataContainer" ] }, { "page": "prepGroup", "title": "prepGroup", "topics": [ "prepGroup" ] }, { "page": "prepHeatData", "title": "prepHeatData", "topics": [ "prepHeatData" ] }, { "page": "prepPCADat", "title": "prepPCADat", "topics": [ "prepPCADat" ] }, { "page": "progress_message", "title": "Build a named list payload for the \"debrowser-progress\" custom message.", "topics": [ "progress_message" ] }, { "page": "push", "title": "push", "topics": [ "push" ] }, { "page": "qc_keep_cols", "title": "Subset a count matrix to a user-selected column list.", "topics": [ "qc_keep_cols" ] }, { "page": "qc_keep_meta_rows", "title": "Subset a sample-metadata data.frame by a user-selected column list.", "topics": [ "qc_keep_meta_rows" ] }, { "page": "qcCooksUI", "title": "qcCooksUI", "topics": [ "qcCooksUI" ] }, { "page": "qcDetectionRateUI", "title": "qcDetectionRateUI", "topics": [ "qcDetectionRateUI" ] }, { "page": "qcDispersionUI", "title": "qcDispersionUI", "topics": [ "qcDispersionUI" ] }, { "page": "qcLibraryDepthUI", "title": "qcLibraryDepthUI", "topics": [ "qcLibraryDepthUI" ] }, { "page": "qcMtPctUI", "title": "qcMtPctUI", "topics": [ "qcMtPctUI" ] }, { "page": "qcSampleDistUI", "title": "qcSampleDistUI", "topics": [ "qcSampleDistUI" ] }, { "page": "qcSizeFactorsUI", "title": "qcSizeFactorsUI", "topics": [ "qcSizeFactorsUI" ] }, { "page": "removeCols", "title": "removeCols", "topics": [ "removeCols" ] }, { "page": "removeExtraCols", "title": "removeExtraCols", "topics": [ "removeExtraCols" ] }, { "page": "require_pkg", "title": "Require a Suggested package, with a friendly error if missing.", "topics": [ "require_pkg" ] }, { "page": "resend_verification_email", "title": "Re-send the verification email for an existing unverified user.", "topics": [ "resend_verification_email" ] }, { "page": "reset_debrowser_password", "title": "Reset a debrowser user's password from the R console.", "topics": [ "reset_debrowser_password" ] }, { "page": "round_vals", "title": "round_vals", "topics": [ "round_vals" ] }, { "page": "run_de", "title": "Dispatch a DE run by method name.", "topics": [ "run_de" ] }, { "page": "run_de_methods", "title": "Run multiple DE methods on the same comparison.", "topics": [ "run_de_methods" ] }, { "page": "run_deseq2", "title": "Run DESeq2 on a count matrix.", "topics": [ "run_deseq2" ] }, { "page": "run_edger", "title": "Run edgeR on a count matrix.", "topics": [ "run_edger" ] }, { "page": "run_gsea", "title": "Run pre-ranked GSEA on a DE result table.", "topics": [ "run_gsea" ] }, { "page": "run_limma", "title": "Run limma-voom on a count matrix.", "topics": [ "run_limma" ] }, { "page": "run_pca", "title": "run_pca", "topics": [ "run_pca" ] }, { "page": "runDE", "title": "runDE", "topics": [ "runDE" ] }, { "page": "runDESeq2", "title": "runDESeq2", "topics": [ "runDESeq2" ] }, { "page": "runEdgeR", "title": "runEdgeR", "topics": [ "runEdgeR" ] }, { "page": "runHeatmap", "title": "runHeatmap", "topics": [ "runHeatmap" ] }, { "page": "runHeatmap2", "title": "runHeatmap2", "topics": [ "runHeatmap2" ] }, { "page": "runLimma", "title": "runLimma", "topics": [ "runLimma" ] }, { "page": "sample_distance_matrix", "title": "Sample-to-sample distance matrix from variance-stabilized counts.", "topics": [ "sample_distance_matrix" ] }, { "page": "search_geneset", "title": "Search a data.frame's `ID` column for a gene-set list.", "topics": [ "search_geneset" ] }, { "page": "select_dataset", "title": "Pick a subset of `rdata` based on the `dataset` filter param.", "topics": [ "select_dataset" ] }, { "page": "selectGroupInfo", "title": "selectGroupInfo", "topics": [ "selectGroupInfo" ] }, { "page": "sepRadio", "title": "sepRadio", "topics": [ "sepRadio" ] }, { "page": "setBatch", "title": "setBatch to skip batch effect correction batch variable set with the filter results", "topics": [ "setBatch" ] }, { "page": "showObj", "title": "showObj", "topics": [ "showObj" ] }, { "page": "size_factor_library_summary", "title": "Per-sample size-factor vs. library-size summary.", "topics": [ "size_factor_library_summary" ] }, { "page": "startDEBrowser", "title": "startDEBrowser", "topics": [ "startDEBrowser" ] }, { "page": "startHeatmap", "title": "startHeatmap", "topics": [ "startHeatmap" ] }, { "page": "textareaInput", "title": "textareaInput", "topics": [ "textareaInput" ] }, { "page": "togglePanels", "title": "togglePanels", "topics": [ "togglePanels" ] }, { "page": "update_progress", "title": "Push a progress update to the browser for one key.", "topics": [ "update_progress" ] } ], "_readme": "https://github.com/bioc/debrowser/raw/HEAD/README.md", "_rundeps": [ "abind", "aisdk", "annotate", "AnnotationDbi", "ape", "aplot", "askpass", "assertthat", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "ca", "cachem", "callr", "caTools", "cli", "cluster", "clusterProfiler", "codetools", "colorspace", "colourpicker", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "dendextend", "DESeq2", "digest", "DOSE", "dplyr", "DT", "edgeR", "egg", "enrichit", "enrichplot", "evaluate", "farver", "fastmap", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "foreach", "formatR", "fs", "futile.logger", "futile.options", "gclus", "gdtools", "genefilter", "generics", "GenomicRanges", "ggforce", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggrepel", "ggtangle", "ggtree", "glue", "GO.db", "GOSemSim", "gplots", "gridExtra", "gridGraphics", "gson", "gtable", "gtools", "heatmaply", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "miniUI", "nlme", "openssl", "org.Hs.eg.db", "otel", "patchwork", "permute", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "processx", "promises", "ps", "purrr", "qap", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "registry", "reshape2", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scatterpie", "Seqinfo", "seriation", "shiny", "shinyBS", "shinyjs", "shinyWidgets", "snow", "sourcetools", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "systemfonts", "tibble", "tidydr", "tidyr", "tidyselect", "tidytree", "tinytex", "treeio", "TSP", "tweenr", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "webshot", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "yulab.utils" ], "_vignettes": [ { "source": "DEBrowser.Rmd", "filename": "DEBrowser.html", "title": "DEBrowser: Interactive Differential Expression Analysis", "author": "Alper Kucukural, Onur Yukselen, Manuel Garber", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick start", "Scriptable analytic core", "The Data Prep pipeline", "Uploading counts and metadata", "Low-count filtering & normalization", "Batch-effect correction", "Choosing comparisons and running DE", "Differential expression engines", "DESeq2", "edgeR", "limma", "Exploring results", "Heatmap clustering & scale", "Bookmarking, export & reproducibility", "AI interpretation (optional)", "Operating system dependencies", "Session information", "References" ], "created": "2016-03-23 22:36:02", "modified": "2026-07-20 02:11:30", "commits": 26 } ], "_score": 8.321822043865241, "_indexed": true, "_nocasepkg": "debrowser", "_universes": [ "bioc", "nephantes", "umms-biocore" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.2", "date": "2026-07-25T09:39:03.000Z", "distro": "resolute", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/60a7ff4611d9068b2b9e9a02404918b2a0826ebb9368c7fbb6c3d7ab3026854a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.6.1", "os": "linux", "version": "1.41.2", "date": "2026-07-25T09:38:10.000Z", "distro": "resolute", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/3899ea3f367d1f8a9b9f02c9cd4c1f81a05a5f163c8050c1a449c00df572bc1f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.5.3", "os": "mac", "version": "1.41.2", "date": "2026-07-25T09:29:39.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/89a2968d934f594292e0b20433208b62836b718d2afb7751db552edbc540066d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.6.1", "os": "mac", "version": "1.41.2", "date": "2026-07-25T09:30:28.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/bba69960d4c2769f879d31d93519fda10e7a0e2bbda20fac7ab67054a72dac35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.2", "date": "2026-07-25T09:37:13.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/5085a29680551d4314e4726670674e48458a46c7c59198f80692c236fa37f5dc", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.7.0", "os": "win", "version": "1.41.2", "date": "2026-07-25T09:35:15.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/a01fb1f8c83f476df949befb9905604d8349bf06e698860a3001140fb69c53f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.5.3", "os": "win", "version": "1.41.2", "date": "2026-07-25T09:36:11.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/cbcb8a72f73c4d882d797ac5d62c4a8292236c91cf6d88f6258803491f634ad1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" }, { "r": "4.6.1", "os": "win", "version": "1.41.2", "date": "2026-07-25T09:34:59.000Z", "commit": "f1190cd970fa9d26b27f8300a0a0a21d83bdf682", "fileid": "https://r2.ropensci.org/b3be0bd1686981262180bf02161d31aee0740873390b704a8343e280a2fa179d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/30152618395" } ] }