iSEE

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: 3.14

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

Installation

To install this package, start R (version "4.1") 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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, SingleCell, Software, Transcription, Transcriptomics, Visualization

Version 2.6.0

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, ggrepel, colourpicker, igraph, vipor, mgcv, graphics, grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize, grid

System Requirements

URL https://github.com/iSEE/iSEE

Bug Reports https://github.com/iSEE/iSEE/issues

Suggests testthat, BiocStyle, knitr, rmarkdown, scRNAseq, TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer, viridis, htmltools

Linking To

Enhances

Depends On Me iSEEu

Imports Me

Suggests Me DuoClustering2018, HCAData, schex, TabulaMurisData, TabulaMurisSenisData

Links To Me

Build Report Build Report