# Interactive Differential Expresion Analysis Browser

## Documentation for package ‘debrowser’ version 1.41.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H I K L M N P Q R S T U

## -- A --

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
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).
ai_chat | Build an ellmer chat object for the configured provider/model.
ai_interpret | Send a redacted analytical question to a configured LLM provider.
all2all | all2all
all2allControlsUI | all2allControlsUI
applyFilters | applyFilters
applyFiltersNew | applyFiltersNew
applyFiltersToMergedComparison | applyFiltersToMergedComparison
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.

## -- B --

barMainPlotControlsUI | barMainPlotControlsUI
batchEffectUI | batchEffectUI Creates a panel to coorect batch effect
batchMethod | batchMethod
BoxMainPlotControlsUI | BoxMainPlotControlsUI

## -- C --

changeClusterOrder | changeClusterOrder
checkCountData | checkCountData
checkMetaData | checkMetaData
clusterData | clusterData
clustFunParamsUI | clustFunParamsUI
compareClust | compareClust
comparisonConcordanceServer | Server for the Comparison Concordance tab.
comparisonConcordanceUI | UI for the Comparison Concordance top-level tab.
comparison_labels | Build unique display labels for a list of comparisons.
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
cutOffSelectionServer | cutOffSelectionServer
cutOffSelectionUI | cutOffSelectionUI
cutoff_presets | Cutoff preset table.

## -- D --

dataLCFUI | dataLCFUI Creates a panel to filter low count genes and regions
dataLoadUI | dataLoadUI
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
detection_rate | Per-sample gene detection rate.
detect_separator | Auto-detect the field separator in a count-data file.
deUI | deUI
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
distFunParamsUI | distFunParamsUI
drawKEGG | drawKEGG
drawPCAExplained | Creates a more detailed plot using the PCA results from the selected dataset.

## -- E --

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.

## -- F --

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|.

## -- G --

generateTestData | generateTestData
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
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.
gmt_to_pathways | Read a GMT file into a named list of gene-symbol vectors.

## -- H --

heatmapControlsUI | heatmapControlsUI
heatmapJScode | heatmapJScode
heatmapServer | heatmapServer
heatmapUI | heatmapUI
hideObj | hideObj
histogramControlsUI | histogramControlsUI

## -- I --

install_cutoff_preset_observers | Install Shiny observers that synchronise a preset-button input with the (padj, log2fc_cutoff) numeric inputs.
IQRPlotControlsUI | IQRPlotControlsUI

## -- K --

kmeansControlsUI | kmeansControlsUI

## -- L --

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.

## -- M --

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.

## -- N --

nes_heatmap_data | Reshape per-comparison GSEA results for the NES heatmap.
niceKmeans | niceKmeans
normalizationMethods | normalizationMethods
normalize_counts | Normalize a count matrix.

## -- P --

palUI | palUI
panel.cor | panel.cor
panel.hist | panel.hist
pcaPlotControlsUI | pcaPlotControlsUI
plotData | plotData
plotMarginsUI | plotMarginsUI
plotSizeMarginsUI | plotSizeMarginsUI
plotSizeUI | plotSizeUI
plotTypeUI | plotTypeUI
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
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

## -- Q --

qcCooksUI | qcCooksUI
qcDetectionRateUI | qcDetectionRateUI
qcDispersionUI | qcDispersionUI
qcLibraryDepthUI | qcLibraryDepthUI
qcMtPctUI | qcMtPctUI
qcSampleDistUI | qcSampleDistUI
qcSizeFactorsUI | qcSizeFactorsUI
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.

## -- R --

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
runDE | runDE
runDESeq2 | runDESeq2
runEdgeR | runEdgeR
runHeatmap | runHeatmap
runHeatmap2 | runHeatmap2
runLimma | runLimma
run_de | Dispatch a DE run by method name.
run_deseq2 | Run DESeq2 on a count matrix.
run_de_methods | Run multiple DE methods on the same comparison.
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

## -- S --

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.
selectGroupInfo | selectGroupInfo
select_dataset | Pick a subset of 'rdata' based on the 'dataset' filter param.
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

## -- T --

textareaInput | textareaInput
togglePanels | togglePanels

## -- U --

update_progress | Push a progress update to the browser for one key.