iSEE

DOI: 10.18129/B9.bioc.iSEE    

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

Interactive SummarizedExperiment Explorer

Bioconductor version: Development (3.15)

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 <kevinrue67 at gmail.com>, Federico Marini <marinif at uni-mainz.de>, Charlotte Soneson <charlottesoneson at gmail.com>, Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 2.7.0
In Bioconductor since BioC 3.7 (R-3.5) (3.5 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
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools
SystemRequirements
Enhances
URL https://github.com/iSEE/iSEE
BugReports https://github.com/iSEE/iSEE/issues
Depends On Me iSEEu
Imports Me
Suggests Me DuoClustering2018, HCAData, schex, TabulaMurisData, TabulaMurisSenisData
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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

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