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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

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) (6 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
System Requirements
URL https://github.com/csoneson/iSEE
Bug Reports https://github.com/csoneson/iSEE/issues
See More
Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray(>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me DuoClustering2018, HCAData, TabulaMurisData
Links To Me
Build Report 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 git@git.bioconductor.org:packages/iSEE
Bioc Package Browser https://code.bioconductor.org/browse/iSEE/
Package Short Url https://bioconductor.org/packages/iSEE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive