iSEE
This is the development version of iSEE; for the stable release version, see iSEE.
All Bioconductor versions of iSEE
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7
Interactive SummarizedExperiment Explorer
Bioconductor version: 3.24 · Package version: 2.25.1
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 gmail.com>
Citation
From within R, enter citation("iSEE"):
Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun. iSEE: Interactive SummarizedExperiment Explorer. doi:10.18129/B9.bioc.iSEE, R package version 2.25.1, https://bioconductor.org/packages/iSEE.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("iSEE")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 2.25.1 |
| License | MIT + file LICENSE |
| URL | https://isee.github.io/iSEE/ |
| Bug Reports | https://github.com/iSEE/iSEE/issues |
| Last updated | 2026-07-13 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8 years) |
| Downloads rank | 356 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/iSEE/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("iSEE")| An introduction to the iSEE interface | HTML | R Script |
| Sharing information across iSEE panels | HTML | R Script |
| Configuring iSEE apps | HTML | R Script |
| Describing the ExperimentColorMap class | HTML | R Script |
| Deploying custom panels in the iSEE interface | HTML | R Script |
| How to use iSEE with big data | HTML | R Script |
| Controlling the iSEE interface using speech recognition | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | iSEE_2.25.1.tar.gz |
| Windows binary (x86_64) | iSEE_2.25.0.zip |
| macOS binary (arm64) | iSEE_2.25.0.tgz |
| macOS binary (x86_64) | iSEE_2.25.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iSEE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iSEE |
| Package Downloads Report | Download Stats |
Dependencies
Depends: SummarizedExperiment, SingleCellExperiment
Imports: methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2 (>= 3.4.0), ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid
Suggests: testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, scrapper, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools, GenomicRanges
Reverse dependencies
Depends On Me (7): iSEEde, iSEEhex, iSEEid, iSEEpathways, iSEEtree, iSEEu, miaDash
Imports Me (3): iSEEfier, iSEEhub, iSEEindex
Suggests Me (6): DuoClustering2018, HCAData, HCATonsilData, schex, TabulaMurisData, TabulaMurisSenisData