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 (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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.
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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | shinyDSP_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | shinyDSP_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/shinyDSP/ |
| Package Short Url | https://bioconductor.org/packages/shinyDSP/ |
| Package Downloads Report | Download Stats |