cytoviewer
This is the development version of cytoviewer; for the stable release version, see cytoviewer.
An interactive multi-channel image viewer for R
Bioconductor version: Development (3.24)
This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.
Author: Lasse Meyer [aut, cre]
, Nils Eling [aut]
Maintainer: Lasse Meyer <lasse.meyer at dqbm.uzh.ch>
citation("cytoviewer")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("cytoviewer")
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("cytoviewer")| Interactive multi-channel image visualization in R | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | GPL-3 |
| Depends | |
| Imports | shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/BodenmillerGroup/cytoviewer |
| Bug Reports | https://github.com/BodenmillerGroup/cytoviewer/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, testthat |
| 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 | cytoviewer_1.13.0.tar.gz |
| Windows Binary (x86_64) | cytoviewer_1.13.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | cytoviewer_1.13.1.tgz |
| macOS Binary (sonoma-arm64) | cytoviewer_1.13.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cytoviewer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cytoviewer |
| Bioc Package Browser | https://code.bioconductor.org/browse/cytoviewer/ |
| Package Short Url | https://bioconductor.org/packages/cytoviewer/ |
| Package Downloads Report | Download Stats |