imcRtools
This is the development version of imcRtools; for the stable release version, see imcRtools.
Methods for imaging mass cytometry data analysis
Bioconductor version: Development (3.24)
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("imcRtools")):Nils Eling. imcRtools: Methods for imaging mass cytometry data analysis. doi:10.18129/B9.bioc.imcRtools, R package version 1.19.2, 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.
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 |
Details
| biocViews | Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial |
| Version | 1.19.2 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), SpatialExperiment |
| Imports | S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scrapper (>= 1.6.0), stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph (>= 2.1.0), SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grid, grDevices |
| System Requirements | |
| URL | https://github.com/BodenmillerGroup/imcRtools |
| Bug Reports | https://github.com/BodenmillerGroup/imcRtools/issues |
See More
| Suggests | CATALYST, tidyr, BiocStyle, knitr, rmarkdown, markdown, RColorBrewer, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | imcRtools_1.19.2.tar.gz |
| Windows Binary (x86_64) | imcRtools_1.19.2.zip |
| macOS Binary (big-sur-x86_64) | imcRtools_1.19.2.tgz |
| macOS Binary (sonoma-arm64) | imcRtools_1.19.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/imcRtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/imcRtools |
| Package Short Url | https://bioconductor.org/packages/imcRtools/ |
| Package Downloads Report | Download Stats |