iSEE
Interactive SummarizedExperiment Explorer
Bioconductor version: Release (3.19)
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, cre] 
, Federico Marini [aut] , Charlotte Soneson [aut] , Aaron Lun [aut]
Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>
citation("iSEE")):
Installation
To install this package, start R (version "4.4") 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. Sharing information across panels | HTML | R Script |
| 3. Configuring iSEE apps | HTML | R Script |
| 4. The ExperimentColorMap Class | HTML | R Script |
| 5. Deploying custom panels | HTML | R Script |
| 6. Using iSEE with big data | HTML | R Script |
| 7. Speech recognition | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization |
| Version | 2.16.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | MIT + file LICENSE |
| Depends | SummarizedExperiment, SingleCellExperiment |
| Imports | methods, BiocGenerics, S4Vectors, utils, stats, shiny, shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, listviewer, ComplexHeatmap, circlize, grid |
| System Requirements | |
| URL | https://github.com/iSEE/iSEE |
| Bug Reports | https://github.com/iSEE/iSEE/issues |
See More
| Suggests | testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools |
| Linking To | |
| Enhances | |
| Depends On Me | iSEEde, iSEEhex, iSEEpathways, iSEEu, OSCA.advanced |
| Imports Me | iSEEfier, iSEEhub, iSEEindex |
| Suggests Me | schex, DuoClustering2018, HCAData, HCATonsilData, TabulaMurisData, TabulaMurisSenisData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iSEE_2.16.0.tar.gz |
| Windows Binary (x86_64) | iSEE_2.16.0.zip |
| macOS Binary (x86_64) | iSEE_2.16.0.tgz |
| macOS Binary (arm64) | iSEE_2.16.0.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 3.19 | Source Archive |