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iSEE

Interactive SummarizedExperiment Explorer


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

BiocManager::install("iSEE")

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

Documentation

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

browseVignettes("iSEE")
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
NEWS Text
LICENSE Text

Details

biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 2.14.0
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, ComplexHeatmap, circlize, grid
System Requirements
URL https://github.com/iSEE/iSEE
Bug Reports https://github.com/iSEE/iSEE/issues
See More
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 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 iSEE_2.14.0.tar.gz
Windows Binary iSEE_2.14.0.zip
macOS Binary (x86_64) iSEE_2.14.0.tgz
macOS Binary (arm64) iSEE_2.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/iSEE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/iSEE
Bioc Package Browser https://code.bioconductor.org/browse/iSEE/
Package Short Url https://bioconductor.org/packages/iSEE/
Package Downloads Report Download Stats