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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../workflows/html/spicyWorkflow.html below:

Bioconductor - spicyWorkflow (development version)

spicyWorkflow

This is the development version of spicyWorkflow; for the stable release version, see spicyWorkflow.

Performing a Spatial Analysis of Multiplexed Tissue Imaging Data

Bioconductor version: Development (3.22)

We have developed an analytical framework for analysing data from high dimensional in situ cytometry assays including CODEX, CycIF, IMC and High Definition Spatial Transcriptomics. This framework makes use of functionality from our Bioconductor packages spicyR, lisaClust, scFeatures, FuseSOM, simpleSeg and ClassifyR and contains most of the key steps which are needed to interrogate the comprehensive spatial information generated by these exciting new technologies including cell segmentation, feature normalisation, cell type identification, micro-environment characterisation, spatial hypothesis testing and patient classification. Ultimately, our modular analysis framework provides a cohesive and accessible entry point into spatially resolved single cell data analysis for any R-based bioinformatician.

Author: Alex Qin [aut], Alexander Nicholls [aut], Nicholas Robertson [aut], Nicolas Canete [aut], Elijah Willie [aut], Ellis Patrick [aut] ORCID: 0000-0002-5253-4747 , SOMS Maintainer [aut, cre]

Maintainer: SOMS Maintainer <maths.bioconductor at sydney.edu.au>

Citation (from within R, enter citation("spicyWorkflow")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("spicyWorkflow")

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("spicyWorkflow")
Details See More Suggests knitr, rmarkdown, BiocStyle, EBImage, cytomapper, ggplot2, ggpubr, lisaClust, spicyR, ClassifyR, scater, dplyr, simpleSeg, FuseSOM, HDF5Array, parallel, tidySingleCellExperiment, SpatialDatasets, Statial, treekoR Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Package Archives

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

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