DOI: 10.18129/B9.bioc.iSEE  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: 3.16

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 "4.2") 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:



HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 2.10.0
In Bioconductor since BioC 3.7 (R-3.5) (5 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, ComplexHeatmap, circlize, grid
Suggests testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools
Depends On Me iSEEhex, iSEEu
Imports Me iSEEhub
Suggests Me DuoClustering2018, HCAData, schex, TabulaMurisData, TabulaMurisSenisData
Links To Me
Build Report  

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

Source Package iSEE_2.10.0.tar.gz
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macOS Binary (x86_64) iSEE_2.10.0.tgz
macOS Binary (arm64) iSEE_2.10.0.tgz
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Source Repository (Developer Access) git clone
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