cytomapper

DOI: 10.18129/B9.bioc.cytomapper    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see cytomapper.

Visualization of highly multiplexed imaging data in R

Bioconductor version: 3.12

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.

Author: Nils Eling [aut, cre] , Nicolas Damond [aut] , Tobias Hoch [ctb]

Maintainer: Nils Eling <nils.eling at dqbm.uzh.ch>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cytomapper")

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("cytomapper")

 

HTML	R Script	Visualization of imaging cytometry data in R
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel
Version	1.2.1
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
License	GPL (>= 2)
Depends	R (>= 4.0), EBImage, SingleCellExperiment, methods
Imports	S4Vectors, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/BodenmillerGroup/cytomapper
BugReports	https://github.com/BodenmillerGroup/cytomapper/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cytomapper_1.2.1.tar.gz
Windows Binary	cytomapper_1.2.1.zip
macOS 10.13 (High Sierra)	cytomapper_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cytomapper
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cytomapper
Package Short Url	https://bioconductor.org/packages/cytomapper/
Package Downloads Report	Download Stats