Bioconductor version: Release (3.17)
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 (from within R,
enter citation("cytoviewer")
):
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("cytoviewer")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cytoviewer")
HTML | R Script | Interactive multi-channel image visualization in R |
Reference Manual | ||
Text | NEWS |
biocViews | DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel |
Version | 1.0.1 |
In Bioconductor since | BioC 3.17 (R-4.3) (< 6 months) |
License | GPL-3 |
Depends | |
Imports | shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment |
LinkingTo | |
Suggests | BiocStyle, knitr, rmarkdown, markdown, testthat |
SystemRequirements | |
Enhances | |
URL | https://github.com/BodenmillerGroup/cytoviewer |
BugReports | https://github.com/BodenmillerGroup/cytoviewer/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | cytoviewer_1.0.1.tar.gz |
Windows Binary | cytoviewer_1.0.1.zip |
macOS Binary (x86_64) | cytoviewer_1.0.1.tgz |
macOS Binary (arm64) | cytoviewer_1.0.1.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 |
Old Source Packages for BioC 3.17 | Source Archive |
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