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 (3.21)
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] (ORCID:
Maintainer: Lasse Meyer <lasse.meyer at dqbm.uzh.ch>
citation("cytoviewer")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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_1.7.0.tar.gz |
| Windows Binary (x86_64) | cytoviewer_1.7.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |