accountDropdownServer   Server: wires the dropdown to current_user,
                        signup modal, signout.
accountDropdownUI       UI: navbar account dropdown.
actionButtonDE          Buttons including Action Buttons and Event
                        Buttons
addDataCols             addDataCols
addID                   addID
ai_chat                 Build an ellmer chat object for the configured
                        provider/model.
ai_interpret            Send a redacted analytical question to a
                        configured LLM provider.
aiInterpretServer       AI interpretation panel server.
aiInterpretUI           AI interpretation panel UI.
aiSettingsServer        Settings server - opens the AI configuration
                        modal on click.
aiSettingsUI            Settings nav_menu UI (mounted in the navbar).
all2all                 all2all
all2allControlsUI       all2allControlsUI
apply_batch_correction
                        Apply batch-effect correction.
apply_de_filters        Apply DE filters and label Up/Down/NS/MV/GS
                        rows.
apply_merged_filters    Apply Up/Down cutoffs across a
                        merged-comparisons table.
applyFilters            applyFilters
applyFiltersNew         applyFiltersNew
applyFiltersToMergedComparison
                        applyFiltersToMergedComparison
barMainPlotControlsUI   barMainPlotControlsUI
batchEffectUI           batchEffectUI Creates a panel to coorect batch
                        effect
batchMethod             batchMethod
BoxMainPlotControlsUI   BoxMainPlotControlsUI
changeClusterOrder      changeClusterOrder
checkCountData          checkCountData
checkMetaData           checkMetaData
clusterData             clusterData
clustFunParamsUI        clustFunParamsUI
compareClust            compareClust
comparison_labels       Build unique display labels for a list of
                        comparisons.
comparisonConcordanceServer
                        Server for the Comparison Concordance tab.
comparisonConcordanceUI
                        UI for the Comparison Concordance top-level
                        tab.
compute_pill_class      Compute the CSS class name for a pill given its
                        progress state.
concordance_sets        Build per-method significant-gene sets.
concordance_summary     Pairwise concordance summary across DE methods.
condSelectServer        Comparison-Selection wizard server.
condSelectUI            Comparison-Selection wizard UI.
cooks_outlier_summary   Per-sample Cook's distance outlier counts.
correctCombat           Correct Batch Effect using Combat in sva
                        package
correctHarman           Correct Batch Effect using Harman
create_debrowser_user   Create a debrowser user from the R console.
customColorsUI          customColorsUI
cutoff_presets          Cutoff preset table.
cutOffSelectionServer   cutOffSelectionServer
cutOffSelectionUI       cutOffSelectionUI
dataLCFUI               dataLCFUI Creates a panel to filter low count
                        genes and regions
dataLoadUI              dataLoadUI
de_assert_count_matrix
                        Validate that x is a non-empty numeric count
                        matrix.
de_card                 de_card
de_direction_summary    Per-entry up / down / total significant gene
                        counts.
de_error                Raise a structured DEBrowser error.
de_eyebrow              de_eyebrow
de_headline             de_headline
de_nav_chip             de_nav_chip
de_progress_label       Render a label suitable for nav_panel(title=)
                        or actionLink(label=) that includes a slot the
                        JS handler can decorate with a progress icon.
de_stat                 de_stat
de_stat_strip           de_stat_strip
de_style_guide          Open the DEBrowser design-system style guide
de_theme                de_theme
de_workbar              de_workbar
debrowserall2all        debrowserall2all
debrowserbarmainplot    debrowserbarmainplot
debrowserbatcheffect    debrowserbatcheffect
debrowserboxmainplot    debrowserboxmainplot
debrowserdataload       debrowserdataload
debrowserdeanalysis     debrowserdeanalysis
debrowserdensityplot    debrowserdensityplot
debrowserheatmap        debrowserheatmap
debrowserhistogram      debrowserhistogram
debrowserIQRplot        debrowserIQRplot
debrowserlowcountfilter
                        debrowserlowcountfilter
debrowsermainplot       debrowsermainplot
debrowserpcaplot        debrowserpcaplot
debrowserqccooks        debrowserqccooks
debrowserqcdetectionrate
                        debrowserqcdetectionrate
debrowserqcdispersion   debrowserqcdispersion
debrowserqclibrarydepth
                        debrowserqclibrarydepth
debrowserqcmtpct        debrowserqcmtpct
debrowserqcsampledist   debrowserqcsampledist
debrowserqcsizefactors
                        debrowserqcsizefactors
default_cutoffs         Default DE significance cutoffs.
dendControlsUI          dendControlsUI
densityPlotControlsUI   densityPlotControlsUI
deServer                deServer
detect_separator        Auto-detect the field separator in a count-data
                        file.
detection_rate          Per-sample gene detection rate.
deUI                    deUI
distFunParamsUI         distFunParamsUI
drawKEGG                drawKEGG
drawPCAExplained        Creates a more detailed plot using the PCA
                        results from the selected dataset.
enrichmentGmtServer     Server for the gene-set source picker.
enrichmentGmtUI         UI for the gene-set source picker (Enrichment
                        tab sidebar).
enrichmentNesHeatmapServer
                        Server for the NES heatmap card.
enrichmentNesHeatmapUI
                        UI for the NES heatmap card.
enrichmentServer        Server for the Enrichment tab.
enrichmentUI            UI for the Enrichment tab.
exportMenuItems         Export menu items (without nav_menu wrapper)
                        for embedding in the account dropdown. Returns
                        a list of '<li>'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.
exportMenuServer        Export menu server - wires download handlers
                        from a state reactive.
exportMenuUI            Export menu UI - navbar dropdown.
fileTypes               fileTypes
fileUploadBox           fileUploadBox
filter_low_counts       Filter low-count rows from a count matrix.
filter_params_from_input
                        Translate a Shiny 'input' reactive into a
                        structured filter-params list.
flag_outliers_2sd       Flag values further than 2 standard deviations
                        from the mean.
fold_to_log2fc          Convert fold-change cutoff to |log2FC|.
generateTestData        generateTestData
get_most_varied         Compute the most-varied genes by coefficient of
                        variation.
get_table_data          Build the (data, padj_colname, fold_colname)
                        tuple for the Tables tab.
getAfterLoadMsg         getAfterLoadMsg
getAll2AllPlotUI        getAll2AllPlotUI
getBarMainPlot          getBarMainPlot
getBarMainPlotUI        getBarMainPlotUI
getBoxMainPlot          getBoxMainPlot
getBoxMainPlotUI        getBoxMainPlotUI
getBSTableUI            getBSTableUI prepares a Modal to put a table
getColors               getColors
getColorShapeSelection
                        getColorShapeSelection
getCompSelection        getCompSelection
getCondMsg              getCondMsg
getCutOffSelection      getCutOffSelection
getDataAssesmentText    getDataAssesmentText DataAssesment text
getDataForTables        getDataForTables get data to fill up tables tab
getDataPreparationText
                        getDataPreparationText DataPreparation text
getDEAnalysisText       getDEAnalysisText DEAnalysis text
getDensityPlot          getDensityPlot
getDensityPlotUI        getDensityPlotUI
getDEResultsUI          getDEResultsUI Creates a panel to visualize DE
                        results
getDomains              getDomains
getDown                 getDown get down regulated data
getDownloadSection      getDownloadSection
getEnrichDO             getEnrichDO
getEnrichGO             getEnrichGO
getEnrichKEGG           getEnrichKEGG
getEntrezIds            getEntrezIds
getEntrezTable          getEntrezTable
getGeneList             getGeneList
getGeneSetData          getGeneSetData
getGOLeftMenu           getGOLeftMenu
getGoPanel              getGoPanel
getGOPlots              getGOPlots
getGSEA                 getGSEA
getHeatmapUI            getHeatmapUI
getHelpButton           getHelpButton prepares a helpbutton for to go
                        to a specific site in the documentation
getHideLegendOnOff      getHideLegendOnOff
getHistogramUI          getHistogramUI
getIntroText            getIntroText Intro text
getIQRPlot              getIQRPlot
getIQRPlotUI            getIQRPlotUI
getJSLine               getJSLine
getKEGGModal            getKEGGModal prepares a modal for KEGG plots
getLeftMenu             getLeftMenu
getLegendColors         getLegendColors
getLegendRadio          getLegendRadio
getLegendSelect         getLegendSelect
getLevelOrder           getLevelOrder
getLogo                 getLogo
getMainPanel            getMainPanel
getMainPlotsLeftMenu    getMainPlotsLeftMenu
getMainPlotUI           getMainPlotUI
getMean                 getMean
getMergedComparison     getMergedComparison
getMostVariedList       getMostVariedList
getNormalizedMatrix     getNormalizedMatrix
getOrganism             getOrganism
getOrganismBox          getOrganismBox
getOrganismPathway      getOrganismPathway
getPCAcontolUpdatesJS   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.
getPCAexplained         getPCAexplained
getPCAPlotUI            getPCAPlotUI
getPCselection          getPCselection
getPlotArea             getPlotArea
getProgramTitle         getProgramTitle
getQAText               getQAText Some questions and answers
getQCLeftMenu           getQCLeftMenu
getQCPanel              getQCPanel
getSampleDetails        getSampleDetails
getSearchData           getSearchData
getSelectedCols         getSelectedCols
getSelectedDatasetInput
                        getSelectedDatasetInput
getSelHeat              getSelHeat
getShapeColor           getShapeColor
getStartPlotsMsg        getStartPlotsMsg
getStartupMsg           getStartupMsg
getTableDetails         getTableDetails
getTableModal           getTableModal prepares table modal for KEGG
getTableStyle           getTableStyle
getTabUpdateJS          getTabUpdateJS
getUp                   getUp get up regulated data
getUpDown               getUpDown get up+down regulated data
getVariationData        getVariationData
gmt_to_pathways         Read a GMT file into a named list of
                        gene-symbol vectors.
heatmapControlsUI       heatmapControlsUI
heatmapJScode           heatmapJScode
heatmapServer           heatmapServer
heatmapUI               heatmapUI
hideObj                 hideObj
histogramControlsUI     histogramControlsUI
install_cutoff_preset_observers
                        Install Shiny observers that synchronise a
                        preset-button input with the (padj,
                        log2fc_cutoff) numeric inputs.
IQRPlotControlsUI       IQRPlotControlsUI
kmeansControlsUI        kmeansControlsUI
lcfMetRadio             lcfMetRadio
library_depth_summary   Per-sample library depth summary.
list_models             List available models for a configured LLM
                        provider.
log2fc_to_fold          Convert |log2FC| cutoff to fold-change cutoff.
mainPlotControlsUI      mainPlotControlsUI
mainScatterNew          mainScatterNew
make_default_metadata   Build a single-condition single-batch metadata
                        data frame.
match_preset            Identify which preset a (padj, log2fc) pair
                        matches.
merge_comparisons       Merge per-comparison DE results into one wide
                        table.
methods_paragraph       Manuscript-ready methods paragraph.
msigdb_pathways         Fetch MSigDB gene sets as a named list of
                        gene-symbol vectors.
mt_pct_per_sample       Per-sample mitochondrial-transcript percentage.
nes_heatmap_data        Reshape per-comparison GSEA results for the NES
                        heatmap.
niceKmeans              niceKmeans
normalizationMethods    normalizationMethods
normalize_counts        Normalize a count matrix.
palUI                   palUI
panel.cor               panel.cor
panel.hist              panel.hist
pcaPlotControlsUI       pcaPlotControlsUI
plot_de_direction_bar   Horizontal bar plot of up / down DEG counts per
                        comparison.
plot_de_pairwise_heatmap
                        Symmetric pairwise heatmap of significant DEG
                        counts between groups.
plot_method_scatter     Pairwise log2FC scatter between two named
                        entries of a DE list.
plot_method_upset       UpSet plot of DE-gene overlap across methods.
plot_pca                plot_pca
plotData                plotData
plotMarginsUI           plotMarginsUI
plotSizeMarginsUI       plotSizeMarginsUI
plotSizeUI              plotSizeUI
plotTypeUI              plotTypeUI
prepDataContainer       Run DE per comparison and return the downstream
                        'dclist' payload.
prepGroup               prepGroup
prepHeatData            prepHeatData
prepPCADat              prepPCADat
progress_message        Build a named list payload for the
                        "debrowser-progress" custom message.
push                    push
qc_keep_cols            Subset a count matrix to a user-selected column
                        list.
qc_keep_meta_rows       Subset a sample-metadata data.frame by a
                        user-selected column list.
qcCooksUI               qcCooksUI
qcDetectionRateUI       qcDetectionRateUI
qcDispersionUI          qcDispersionUI
qcLibraryDepthUI        qcLibraryDepthUI
qcMtPctUI               qcMtPctUI
qcSampleDistUI          qcSampleDistUI
qcSizeFactorsUI         qcSizeFactorsUI
removeCols              removeCols
removeExtraCols         removeExtraCols
require_pkg             Require a Suggested package, with a friendly
                        error if missing.
resend_verification_email
                        Re-send the verification email for an existing
                        unverified user.
reset_debrowser_password
                        Reset a debrowser user's password from the R
                        console.
round_vals              round_vals
run_de                  Dispatch a DE run by method name.
run_de_methods          Run multiple DE methods on the same comparison.
run_deseq2              Run DESeq2 on a count matrix.
run_edger               Run edgeR on a count matrix.
run_gsea                Run pre-ranked GSEA on a DE result table.
run_limma               Run limma-voom on a count matrix.
run_pca                 run_pca
runDE                   runDE
runDESeq2               runDESeq2
runEdgeR                runEdgeR
runHeatmap              runHeatmap
runHeatmap2             runHeatmap2
runLimma                runLimma
sample_distance_matrix
                        Sample-to-sample distance matrix from
                        variance-stabilized counts.
search_geneset          Search a data.frame's 'ID' column for a
                        gene-set list.
select_dataset          Pick a subset of 'rdata' based on the 'dataset'
                        filter param.
selectGroupInfo         selectGroupInfo
sepRadio                sepRadio
setBatch                setBatch to skip batch effect correction batch
                        variable set with the filter results
showObj                 showObj
size_factor_library_summary
                        Per-sample size-factor vs. library-size
                        summary.
startDEBrowser          startDEBrowser
startHeatmap            startHeatmap
textareaInput           textareaInput
togglePanels            togglePanels
update_progress         Push a progress update to the browser for one
                        key.
