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Interactive SummarizedExperiment Explorer

Bioconductor version: Release (3.19)

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Author: Kevin Rue-Albrecht [aut, cre] , Federico Marini [aut] , Charlotte Soneson [aut] , Aaron Lun [aut]

Maintainer: Kevin Rue-Albrecht <kevinrue67 at>

Citation (from within R, enter citation("iSEE")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. The iSEE User's Guide HTML R Script
2. Sharing information across panels HTML R Script
3. Configuring iSEE apps HTML R Script
4. The ExperimentColorMap Class HTML R Script
5. Deploying custom panels HTML R Script
6. Using iSEE with big data HTML R Script
7. Speech recognition HTML R Script
Reference Manual PDF


biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 2.16.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License MIT + file LICENSE
Depends SummarizedExperiment, SingleCellExperiment
Imports methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid
System Requirements
Bug Reports
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Suggests testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools
Linking To
Depends On Me iSEEde, iSEEhex, iSEEpathways, iSEEu, OSCA.advanced
Imports Me iSEEfier, iSEEhub, iSEEindex
Suggests Me schex, DuoClustering2018, HCAData, HCATonsilData, TabulaMurisData, TabulaMurisSenisData
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package iSEE_2.16.0.tar.gz
Windows Binary
macOS Binary (x86_64) iSEE_2.16.0.tgz
macOS Binary (arm64) iSEE_2.16.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive