iSEE

DOI: 10.18129/B9.bioc.iSEE    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") 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. The ExperimentColorMap Class
HTML	R Script	3. Configuring iSEE apps
HTML	R Script	4. Deploying custom panels
HTML	R Script	5. Speech recognition
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	MIT + file LICENSE
Depends	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, HCAData, TabulaMurisData
Links To Me
Build Report

Package Archives

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

Source Package	iSEE_1.4.0.tar.gz
Windows Binary	iSEE_1.4.0.zip
Mac OS X 10.11 (El Capitan)	iSEE_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/iSEE
Source Repository (Developer Access)	git clone [email protected]:packages/iSEE
Package Short Url	https://bioconductor.org/packages/iSEE/
Package Downloads Report	Download Stats