imcRtools
Methods for imaging mass cytometry data analysis
Bioconductor version: 3.23 · Package version: 1.18.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("imcRtools")Details
| Maintainer | Daniel Schulz <daniel.schulz@uzh.ch> |
| Author | Nils Eling [aut], Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb, cre] (ORCID: <https://orcid.org/0000-0002-0913-1678>), Lasse Meyer [ctb], Lutz Marlene [ctb], Schiller Chiara [ctb], Ibañez Victor [ctb] |
| License | GPL-3 |
| URL | https://github.com/BodenmillerGroup/imcRtools |
| Bug Reports | https://github.com/BodenmillerGroup/imcRtools/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial |
| Package Short Url | https://bioconductor.org/packages/imcRtools/ |
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 1.18.1, https://bioconductor.org/packages/imcRtools.
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 | imcRtools_1.18.1.tar.gz |
| Windows binary (x86_64) | imcRtools_1.18.1.zip |
| macOS binary (arm64) | imcRtools_1.18.1.tgz |
| macOS binary (x86_64) | imcRtools_1.18.1.tgz |
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