cytomapper
Visualization of highly multiplexed imaging data in R
Bioconductor version: 3.23 · Package version: 1.24.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cytomapper")Details
| Maintainer | Lasse Meyer <lasse.meyer@dqbm.uzh.ch> |
| Author | Nils Eling [aut] (ORCID: <https://orcid.org/0000-0002-4711-1176>), Nicolas Damond [aut] (ORCID: <https://orcid.org/0000-0003-3027-8989>), Tobias Hoch [ctb], Lasse Meyer [cre, ctb] (ORCID: <https://orcid.org/0000-0002-1660-1199>) |
| License | GPL (>= 2) |
| URL | https://github.com/BodenmillerGroup/cytomapper |
| Bug Reports | https://github.com/BodenmillerGroup/cytomapper/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/cytomapper/ |
Citation
From within R, enter citation("cytomapper"):
Nils Eling, Nicolas Damond. cytomapper: Visualization of highly multiplexed imaging data in R. doi:10.18129/B9.bioc.cytomapper, R package version 1.24.0, https://bioconductor.org/packages/cytomapper.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | cytomapper_1.24.0.tar.gz |
| Windows binary (x86_64) | cytomapper_1.24.0.zip |
| macOS binary (arm64) | cytomapper_1.24.0.tgz |
| macOS binary (x86_64) | cytomapper_1.24.0.tgz |
Dependencies
Depends: R (>= 4.0), EBImage, SingleCellExperiment, methods
Imports: SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls
Suggests: BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest
Reverse dependencies
Depends On Me (1): imcdatasets
Imports Me (3): cytoviewer, imcRtools, simpleSeg
Suggests Me (1): SpatialDatasets