spicyWorkflow

Performing a Spatial Analysis of Multiplexed Tissue Imaging Data

Bioconductor version: Release (3.19)

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: Alexander Nicholls [aut], Nicholas Robertson [aut], Nicolas Canete [aut], Elijah Willie [aut], Ellis Patrick [aut] , 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 "4.4") and enter:


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

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")

Introduction to a spicy workflow

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R Script

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Details

biocViews	ImmunoOncologyWorkflow, SpatialWorkflow, Workflow
Version	1.3.1
License	GPL-3
Depends	R (>= 4.3.0)
Imports
System Requirements
URL	https://github.com/SydneyBioX/spicyWorkflow
Bug Reports	https://github.com/SydneyBioX/spicyWorkflow/issues

Suggests	knitr, rmarkdown, BiocStyle, EBImage, cytomapper, ggplot2, ggpubr, lisaClust, spicyR, ClassifyR, scater, dplyr, simpleSeg, FuseSOM, HDF5Array, parallel, tidySingleCellExperiment
Linking To
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Package Archives

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

Source Package	spicyWorkflow_1.3.1.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/spicyWorkflow
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spicyWorkflow
Package Short Url	https://bioconductor.org/packages/spicyWorkflow/
Package Downloads Report	Download Stats