iSEE
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see iSEE.
Interactive SummarizedExperiment Explorer
Bioconductor version: 3.11
Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special 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 "4.0") 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 | 2.0.0 |
| 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, graphics, grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize |
| System Requirements | |
| URL | https://github.com/iSEE/iSEE |
| Bug Reports | https://github.com/iSEE/iSEE/issues |
See More
| Suggests | testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray, RColorBrewer, viridis, htmltools |
| Linking To | |
| Enhances | |
| Depends On Me | iSEEu |
| Imports Me | |
| Suggests Me | DuoClustering2018, HCAData, schex, TabulaMurisData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iSEE_2.0.0.tar.gz |
| Windows Binary | iSEE_2.0.0.zip |
| macOS 10.13 (High Sierra) | iSEE_2.0.0.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 3.11 | Source Archive |