shinyDSP
This is the released version of shinyDSP; for the devel version, see shinyDSP.
A Shiny App For Visualizing Nanostring GeoMx DSP Data
Bioconductor version: Release (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]
, Marco Mura [aut, fnd]
Maintainer: Seung J. Kim <skim823 at uwo.ca>
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| 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 |