iSEE

DOI: 10.18129/B9.bioc.iSEE    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: 3.7

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

Maintainer: Federico Marini <marinif at uni-mainz.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("iSEE")

Documentation

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

browseVignettes("iSEE")

 

HTML	R Script	iSEE User's Guide
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, SingleCell, Software, Transcription, Transcriptomics, Visualization
Version	1.0.1
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, Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools
SystemRequirements
Enhances	ExperimentHub
URL	https://github.com/csoneson/iSEE
BugReports	https://github.com/csoneson/iSEE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	iSEE_1.0.1.tar.gz
Windows Binary	iSEE_1.0.1.zip
Mac OS X 10.11 (El Capitan)	iSEE_1.0.1.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