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Showing content from http://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/iSEE.html below:

Bioconductor - iSEE (development version)

iSEE

This is the development version of iSEE; for the stable release version, see iSEE.

Interactive SummarizedExperiment Explorer

Bioconductor version: Development (3.22)

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] ORCID: 0000-0003-3899-3872 , Federico Marini [aut] ORCID: 0000-0003-3252-7758 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169 , Aaron Lun [aut] ORCID: 0000-0002-3564-4813

Maintainer: Kevin Rue-Albrecht <kevinrue67 at gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews CellBasedAssays, Clustering, DimensionReduction, FeatureExtraction, GUI, GeneExpression, ImmunoOncology, ShinyApps, SingleCell, Software, Transcription, Transcriptomics, Visualization Version 2.21.1 In Bioconductor since BioC 3.7 (R-3.5) (7 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://isee.github.io/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, GenomicRanges Linking To Enhances Depends On Me iSEEde, iSEEhex, iSEEpathways, iSEEtree, iSEEu, miaDash, 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.

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