imcRtools
Methods for imaging mass cytometry data analysis
Bioconductor version: Release (3.20)
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]
Maintainer: Daniel Schulz <daniel.schulz at uzh.ch>
citation("imcRtools")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.1), SpatialExperiment |
| Imports | S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scuttle, 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 |
| System Requirements | |
| URL | https://github.com/BodenmillerGroup/imcRtools |
| Bug Reports | https://github.com/BodenmillerGroup/imcRtools/issues |
See More
| Suggests | CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | spicyR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | imcRtools_1.12.0.tar.gz |
| Windows Binary (x86_64) | imcRtools_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | imcRtools_1.12.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/imcRtools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/imcRtools |
| Bioc Package Browser | https://code.bioconductor.org/browse/imcRtools/ |
| Package Short Url | https://bioconductor.org/packages/imcRtools/ |
| Package Downloads Report | Download Stats |