imcRtools

DOI: 10.18129/B9.bioc.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 (3.15)

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]

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

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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")

 

HTML R Script Tools for IMC data analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial
Version 1.1.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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
LinkingTo
Suggests CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat
SystemRequirements
Enhances
URL https://github.com/BodenmillerGroup/imcRtools
BugReports https://github.com/BodenmillerGroup/imcRtools/issues
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_1.1.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) imcRtools_1.1.1.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

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