geyser

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see geyser.

Gene Expression displaYer of SummarizedExperiment in R

Bioconductor version: 3.21

Lightweight Expression displaYer (plotter / viewer) of SummarizedExperiment object in R. This package provides a quick and easy Shiny-based GUI to empower a user to use a SummarizedExperiment object to view (gene) expression grouped from the sample metadata columns (in the `colData` slot). Feature expression can either be viewed with a box plot or a heatmap.

Author: David McGaughey [aut, cre] ORCID iD ORCID: 0000-0002-9224-2888

Maintainer: David McGaughey <mcgaughey at gmail.com>

Citation (from within R, enter citation("geyser")):

Installation

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


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

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("geyser")

Gene_Expression_Plotting_GUI HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GUI, GeneExpression, ShinyApps, Software

Version 1.0.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License CC0

Depends R (>= 3.5.0)

Imports bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT, ggbeeswarm, ggplot2, htmltools, magrittr, shiny, SummarizedExperiment, tibble, tidyselect, tidyr

System Requirements

URL https://github.com/davemcg/geyser

Bug Reports https://github.com/davemcg/geyser/issues

Suggests airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package geyser_1.0.0.tar.gz

Windows Binary (x86_64) geyser_1.0.0.zip

macOS Binary (x86_64) geyser_1.0.0.tgz

macOS Binary (arm64) geyser_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/geyser

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/geyser

Bioc Package Browser https://code.bioconductor.org/browse/geyser/

Package Short Url https://bioconductor.org/packages/geyser/

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