spicyR
This is the development version of spicyR; for the stable release version, see spicyR.
Test Changes in the Co-Localisation of Cell Types Between Groups of Patients
Bioconductor version: Development (3.24)
spicyR tests whether the spatial co-localisation of pairs of cell types differs between groups of patients, or is associated with patient outcome, in cell-resolution spatial omics data (imaging mass cytometry, CODEX, MIBI, Xenium, CosMx and others). Its default method, spicyR Cell, counts the cells of one type within a radius of each cell of another and compares the count with its exact expectation under random labelling of the observed cells. Images are combined within patients by a frailty generalised estimating equation, and differences are tested with a small-sample cluster-robust (CR2) variance with patients as the units. Covariates, several conditions, several radii and survival outcomes are supported, and the original image-level test is kept as an option. The computations run in a C++ core shared with the Python package spicyr.
Author: Nicolas Canete [aut], Ellis Patrick [aut, cre], Sadiq Dohadwalla [aut], Elijah Willie [aut], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("spicyR")):Nicolas Canete, Ellis Patrick, Sadiq Dohadwalla, Elijah Willie. spicyR: Test Changes in the Co-Localisation of Cell Types Between Groups of Patients. doi:10.18129/B9.bioc.spicyR, R package version 1.99.11, https://bioconductor.org/packages/spicyR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("spicyR")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("spicyR")| The original image-level test (method = "image") | HTML | R Script |
| Introduction to spicyR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial, Survival |
| Version | 1.99.11 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.5.0) |
| Imports | Rcpp, methods, stats, utils, grDevices, grid, splines, parallel, ggplot2, S4Vectors, survival |
| System Requirements | C++17 |
| URL | https://sydneybiox.github.io/spicyR/ https://github.com/SydneyBioX/spicyR |
| Bug Reports | https://github.com/SydneyBioX/spicyR/issues |
See More
| Suggests | SummarizedExperiment, plotly, dplyr, SingleCellExperiment, SpatialExperiment, lmerTest, lme4, scam, coxme, spatstat.geom, spatstat.explore, BiocParallel, SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | OSTA, Statial |
| Suggests Me | lisaClust |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spicyR_1.99.11.tar.gz |
| Windows Binary (x86_64) | spicyR_1.99.6.zip |
| macOS Binary (big-sur-x86_64) | spicyR_1.99.11.tgz |
| macOS Binary (sonoma-arm64) | spicyR_1.99.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spicyR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spicyR |
| Package Short Url | https://bioconductor.org/packages/spicyR/ |
| Package Downloads Report | Download Stats |