Package: debrowser 1.41.2

Alper Kucukural

debrowser: Interactive Differential Expresion Analysis Browser

Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.

Authors:Alper Kucukural [aut, cre], Onur Yukselen [aut], Manuel Garber [aut]

debrowser_1.41.2.tar.gz
debrowser_1.41.2.zip(r-4.7-any)debrowser_1.41.2.zip(r-4.6-any)debrowser_1.41.2.zip(r-4.5-any)
debrowser_1.41.2.tgz(r-4.6-any)debrowser_1.41.2.tgz(r-4.5-any)
debrowser_1.41.2.tar.gz(r-4.7-any)debrowser_1.41.2.tar.gz(r-4.6-any)
debrowser_1.41.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
debrowser/json (API)

# Install 'debrowser' in R:

install.packages('debrowser', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/umms-biocore/debrowser/issues

On BioConductor:debrowser-1.41.0(bioc 3.24)debrowser-1.40.0(bioc 3.23)

sequencing chipseq rnaseq differentialexpression geneexpression clustering immunooncology

8.32 score 62 stars 141 scripts 2 mentions 277 exports 191 dependencies

Last updated from:f1190cd970. Checks:1 FAILURE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	FAILURE	283
linux-devel-x86_64	OK	740
source / vignettes	OK	460
linux-release-x86_64	OK	673
macos-release-arm64	OK	376
macos-oldrel-arm64	OK	332
windows-devel-x86_64	OK	481
windows-release-x86_64	OK	504
windows-oldrel-x86_64	OK	516
wasm-release	OK	270

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

Dependencies: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

DEBrowser: Interactive Differential Expression Analysis

Rendered fromDEBrowser.Rmdusingknitr::rmarkdown

Last update: 2026-07-20
Started: 2016-03-23

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

Package: debrowser 1.41.2

debrowser: Interactive Differential Expresion Analysis Browser

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)