cytomapper
This is the released version of cytomapper; for the devel version, see cytomapper.
Visualization of highly multiplexed imaging data in R
Bioconductor version: Release (3.23)
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]
, Nicolas Damond [aut]
, Tobias Hoch [ctb], Lasse Meyer [cre, ctb]
Maintainer: Lasse Meyer <lasse.meyer at dqbm.uzh.ch>
citation("cytomapper")):
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")
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")| On disk storage of images | HTML | R Script |
| Visualization of imaging cytometry data in R | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>= 2) |
| 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 |
| System Requirements | |
| URL | https://github.com/BodenmillerGroup/cytomapper |
| Bug Reports | https://github.com/BodenmillerGroup/cytomapper/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | cytoviewer, imcRtools, simpleSeg |
| Suggests Me | SpatialDatasets |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow 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 (64-bit only) |
| macOS Binary (big-sur-x86_64) | cytomapper_1.24.0.tgz |
| macOS Binary (sonoma-arm64) | cytomapper_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cytomapper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cytomapper |
| Bioc Package Browser | https://code.bioconductor.org/browse/cytomapper/ |
| Package Short Url | https://bioconductor.org/packages/cytomapper/ |
| Package Downloads Report | Download Stats |