iSEE

This is the development version of iSEE; for the stable release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: Development (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 gmail.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("iSEE")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version	2.15.1
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
URL	https://github.com/iSEE/iSEE
Bug Reports	https://github.com/iSEE/iSEE/issues

Suggests	testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools
Linking To
Enhances
Depends On Me	iSEEde, iSEEhex, iSEEpathways, iSEEu
Imports Me	iSEEfier, iSEEhub, iSEEindex
Suggests Me	DuoClustering2018, HCAData, HCATonsilData, schex, TabulaMurisData, TabulaMurisSenisData
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/iSEE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/iSEE
Package Short Url	https://bioconductor.org/packages/iSEE/
Package Downloads Report	Download Stats