Interactive Differential Expresion Analysis Browser

Documentation for package ‘debrowser’ version 1.41.1

Help Pages

-- 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

-- 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.