iSEE

DOI: 10.18129/B9.bioc.iSEE    

Interactive SummarizedExperiment Explorer

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

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
Text   LICENSE

Details

biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 2.2.0
In Bioconductor since BioC 3.7 (R-3.5) (2.5 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
Links To Me
Build Report  

Package Archives

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

Source Package iSEE_2.2.0.tar.gz
Windows Binary iSEE_2.2.0.zip
macOS 10.13 (High Sierra) iSEE_2.2.0.tgz
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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