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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 (3.20)

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 (from within R, enter citation("imcRtools")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
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Depends On Me
Imports Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package imcRtools_1.11.0.tar.gz
Windows Binary imcRtools_1.11.0.zip (64-bit only)
macOS Binary (x86_64) imcRtools_1.11.0.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