iSEE

DOI: 10.18129/B9.bioc.iSEE    

Interactive SummarizedExperiment Explorer

Bioconductor version: Release (3.8)

Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Author: Kevin Rue-Albrecht [aut], Federico Marini [aut], Charlotte Soneson [aut, cre], Aaron Lun [aut]

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("iSEE", version = "3.8")

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. The ExperimentColorMap Class
HTML R Script 3. Configuring iSEE apps
HTML R Script 4. Deploying custom panels
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version 1.2.0
License MIT + file LICENSE
Depends R (>= 3.5), SummarizedExperiment, SingleCellExperiment
Imports methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, colourpicker, igraph, vipor, mgcv, reshape2, rentrez, AnnotationDbi, graphics, grDevices, viridisLite, cowplot, scales, dplyr
LinkingTo
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray(>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools
SystemRequirements
Enhances
URL https://github.com/csoneson/iSEE
BugReports https://github.com/csoneson/iSEE/issues
Depends On Me
Imports Me
Suggests Me DuoClustering2018, TabulaMurisData
Links To Me
Build Report  

Package Archives

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

Source Package iSEE_1.2.0.tar.gz
Windows Binary iSEE_1.2.0.zip
Mac OS X 10.11 (El Capitan) iSEE_1.2.0.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 http://bioconductor.org/packages/iSEE/
Package Downloads Report Download Stats

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