recipe bioconductor-imcrtools

Methods for imaging mass cytometry data analysis

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/imcRtools.html

License:

GPL-3

Recipe:

/bioconductor-imcrtools/meta.yaml

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.

package bioconductor-imcrtools

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-biocneighbors >=1.16.0,<1.17.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-cytomapper >=1.10.0,<1.11.0

• bioconductor-ebimage >=4.40.0,<4.41.0

• bioconductor-matrixgenerics >=1.10.0,<1.11.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-scuttle >=1.8.0,<1.9.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-spatialexperiment >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-abind

• r-base >=4.2,<4.3.0a0

• r-concaveman

• r-data.table

• r-distances

• r-dplyr

• r-dt

• r-ggplot2

• r-ggraph

• r-igraph

• r-magrittr

• r-pheatmap

• r-readr

• r-rtriangle

• r-sf

• r-stringr

• r-tidygraph

• r-tidyselect

• r-viridis

• r-vroom

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-imcrtools

and update with:

conda update bioconductor-imcrtools

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-imcrtools:<tag>

(see bioconductor-imcrtools/tags for valid values for <tag>)

Download stats

Link to this page

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