imcRtools
This is the development version of imcRtools; for the stable release version, see imcRtools.
All Bioconductor versions of imcRtools
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Methods for imaging mass cytometry data analysis
Bioconductor version: 3.24 · Package version: 1.19.1
This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
Author: Nils Eling [aut], Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb, cre] 
, Lasse Meyer [ctb], Lutz Marlene [ctb], Schiller Chiara [ctb], Ibañez Victor [ctb]
Maintainer: Daniel Schulz <daniel.schulz at uzh.ch>
Citation
From within R, enter citation("imcRtools"):
Nils Eling. imcRtools: Methods for imaging mass cytometry data analysis. doi:10.18129/B9.bioc.imcRtools, R package version 1.19.1, https://bioconductor.org/packages/imcRtools.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("imcRtools")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.19.1 |
| License | GPL-3 |
| URL | https://github.com/BodenmillerGroup/imcRtools |
| Bug Reports | https://github.com/BodenmillerGroup/imcRtools/issues |
| Last updated | 2026-05-09 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 519 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial |
| Package Short Url | https://bioconductor.org/packages/imcRtools/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("imcRtools")| Tools for IMC data analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | imcRtools_1.19.1.tar.gz |
| Windows binary (x86_64) | imcRtools_1.19.1.zip |
| macOS binary (arm64) | imcRtools_1.19.1.tgz |
| macOS binary (x86_64) | imcRtools_1.19.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/imcRtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/imcRtools |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1), SpatialExperiment
Imports: S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scrapper, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices
Suggests: CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat
Reverse dependencies
Suggests Me (1): spicyR