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imcRtools

Methods for imaging mass cytometry data analysis

Bioconductor version: Release (3.17)

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, cre] , Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb], Lasse Meyer [ctb]

Maintainer: Nils Eling <nils.eling at dqbm.uzh.ch>

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

Installation

To install this package, start R (version "4.3") 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 PDF
NEWS Text

Details

biocViews Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial
Version 1.6.3
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Linking To
Suggests CATALYST, grid, BiocStyle, knitr, rmarkdown, markdown, testthat
System Requirements
Enhances
URL https://github.com/BodenmillerGroup/imcRtools
Bug Reports https://github.com/BodenmillerGroup/imcRtools/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package imcRtools_1.6.3.tar.gz
Windows Binary imcRtools_1.6.3.zip
macOS Binary (x86_64) imcRtools_1.6.3.tgz
macOS Binary (arm64) imcRtools_1.6.3.tgz
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
Old Source Packages for BioC 3.17 Source Archive