Package: imcRtools 1.11.0

Daniel Schulz

imcRtools: Methods for imaging mass cytometry data analysis

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.

Authors:Nils Eling [aut], Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb, cre], Lasse Meyer [ctb]

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NEWS

# Install 'imcRtools' in R:

install.packages('imcRtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bodenmillergroup/imcrtools/issues

On BioConductor:imcRtools-1.11.0(bioc 3.20)imcRtools-1.10.0(bioc 3.19)

bioconductor-package

21 exports 1.24 score 177 dependencies

Last updated 2 months agofrom:ddbfcd9f5e

Exports:aggregateNeighbors binAcrossPixels buildSpatialGraph countInteractions detectCommunity detectSpatialContext filterPixels filterSpatialContext findBorderCells minDistToCells patchDetection patchSize plotSpatial plotSpatialContext plotSpotHeatmap read_cpout read_steinbock readImagefromTXT readSCEfromTXT show_cpout_features testInteractions

Dependencies:abind askpass base64enc beachmat beeswarm BH Biobase BiocFileCache BiocGenerics BiocNeighbors BiocParallel bit bit64 bitops blob bslib cachem class classInt cli clipr codetools colorspace commonmark concaveman cpp11 crayon crosstalk curl cytomapper data.table DBI dbplyr DelayedArray DelayedMatrixStats digest distances dplyr DT e1071 EBImage evaluate fansi farver fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable HDF5Array highr hms htmltools htmlwidgets httpuv httr igraph IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnls openssl pheatmap pillar pkgconfig plogr png polyclip prettyunits progress promises proxy purrr R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RcppEigen RcppHNSW RCurl readr rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite RTriangle s2 S4Arrays S4Vectors sass scales scuttle sf shiny shinydashboard SingleCellExperiment snow sourcetools sp SparseArray sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment svglite svgPanZoom sys systemfonts terra tibble tidygraph tidyr tidyselect tiff tinytex tweenr tzdb UCSC.utils units utf8 V8 vctrs vipor viridis viridisLite vroom withr wk xfun xtable XVector yaml zlibbioc

Tools for IMC data analysis

Nils Eling, Lasse Meyer, Daniel Schulz

Rendered fromimcRtools.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-06-20
Started: 2020-12-17

Help page	Topics
Function to aggregate all neighbors of each cell.	aggregateNeighbors
Aggregate consecutive pixels per single-metal spot	binAcrossPixels
Builds an interaction graph based on the cells' locations	buildSpatialGraph
Summarizes cell-cell interactions within grouping levels (e.g. images)	countInteractions
Detect the spatial community of each cell	detectCommunity
Detect the spatial context of each cell based on its neighborhood	detectSpatialContext
Filter pixels based on their assigned masses	filterPixels
Filter spatial contexts	filterSpatialContext
Find cells at the image border	findBorderCells
Function to calculate minimal distance to cells of interest	minDistToCells
Function to detect patches containing defined cell types	patchDetection
Function to compute the area of c3ll patches	patchSize
Visualizes the spatial locations and interactions of cells	plotSpatial
Plot spatial context graph	plotSpatialContext
Summarizes and visualizes the pixel intensities per spot and channel	plotSpotHeatmap
Reads in single-cell data generated by the ImcSegmentationPipeline	read_cpout
Reads in single-cell data generated by the steinbock pipeline	read_steinbock
Reads one or multiple .txt files into a CytoImageList object	readImagefromTXT
Generates a SingleCellExperiment from .txt files	readSCEfromTXT
Display all features measured by CellProfiler.	show_cpout_features
Tests if cell types interact more or less frequently than random	testInteractions

Package: imcRtools 1.11.0

imcRtools: Methods for imaging mass cytometry data analysis

Tools for IMC data analysis

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