shinyDSP

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

A Shiny App For Visualizing Nanostring GeoMx DSP Data

Bioconductor version: 3.21

This package is a Shiny app for interactively analyzing and visualizing Nanostring GeoMX Whole Transcriptome Atlas data. Users have the option of exploring a sample data to explore this app's functionality. Regions of interest (ROIs) can be filtered based on any user-provided metadata. Upon taking two or more groups of interest, all pairwise and ANOVA-like testing are automatically performed. Available ouputs include PCA, Volcano plots, tables and heatmaps. Aesthetics of each output are highly customizable.

Author: Seung J. Kim [aut, cre] ORCID iD ORCID: 0000-0001-5263-0758 , Marco Mura [aut, fnd]

Maintainer: Seung J. Kim <skim823 at uwo.ca>

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

Installation

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


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

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("shinyDSP")

shinyDSP HTML R Script

shinyDSP_secondary HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, ShinyApps, Software, Spatial, Transcriptomics

Version 1.0.3

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

License MIT + file LICENSE

Depends R (>= 4.5)

Imports AnnotationHub, BiocGenerics, bsicons, bslib, circlize, ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub, ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma, magrittr, pals, readr, S4Vectors, scales, scater, shiny, shinycssloaders, shinyjs, shinyvalidate, shinyWidgets, SingleCellExperiment, standR, stats, stringr, SummarizedExperiment, tibble, tidyr, utils, withr

System Requirements

URL https://github.com/kimsjune/shinyDSP http://joonkim.ca/shinyDSP/

Bug Reports https://github.com/kimsjune/shinyDSP/issues

Suggests BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package shinyDSP_1.0.3.tar.gz

Windows Binary (x86_64) shinyDSP_1.0.3.zip

macOS Binary (x86_64) shinyDSP_1.0.3.tgz

macOS Binary (arm64) shinyDSP_1.0.3.tgz

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

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

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

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

Package Downloads Report Download Stats

Old Source Packages for BioC 3.21 Source Archive