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("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 | ||
| 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 |