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spicyWorkflow
This package is for version 3.22 of Bioconductor.This package has been removed from Bioconductor.For the last stable, up-to-date release version, seespicyWorkflow.
Performing a Spatial Analysis of Multiplexed Tissue Imaging Data
Bioconductor version: Release (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("spicyWorkflow")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("spicyWorkflow")For older versions of R, please refer to the appropriateBioconductor 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 | HTML | R Script |
Details
| biocViews | ImmunoOncologyWorkflow,SpatialWorkflow,Workflow |
| Version | 1.9.0 |
| 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 |
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 | |
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Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | spicyWorkflow_1.9.0.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 |