shinyDSP
This is the released version of shinyDSP; for the devel version, see shinyDSP.
All Bioconductor versions of shinyDSP
3.24 (devel), 3.23 (release), 3.22, 3.21
A Shiny App For Visualizing Nanostring GeoMx DSP Data
Bioconductor version: 3.23 · Package version: 1.4.0
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] 
, Marco Mura [aut, fnd]
Maintainer: Seung J. Kim <skim823 at uwo.ca>
Citation
From within R, enter citation("shinyDSP"):
Seung J. Kim, Marco Mura. shinyDSP: A Shiny App For Visualizing Nanostring GeoMx DSP Data. doi:10.18129/B9.bioc.shinyDSP, R package version 1.4.0, https://bioconductor.org/packages/shinyDSP.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.4.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/kimsjune/shinyDSP http://joonkim.ca/shinyDSP/ |
| Bug Reports | https://github.com/kimsjune/shinyDSP/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 2062 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, ShinyApps, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/shinyDSP/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("shinyDSP")| shinyDSP tutorial | HTML | R Script |
| shinyDSP internal data processing pipeline explained | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | shinyDSP_1.4.0.tar.gz |
| Windows binary (x86_64) | shinyDSP_1.4.0.zip |
| macOS binary (arm64) | shinyDSP_1.4.0.tgz |
| macOS binary (x86_64) | shinyDSP_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/shinyDSP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/shinyDSP |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0)