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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| Introduction to spicyR | HTML | R Script |
| The original image-level test (method = "image") | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CellBasedAssays, SingleCell, Software, Spatial, Survival |
| Version | 1.99.6 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.6.0) |
| 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, concaveman, BiocParallel, SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppEigen |
| Enhances | |
| Depends On Me | |
| Imports Me | lisaClust, OSTA |
| Suggests Me | Statial |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spicyR_1.99.6.tar.gz |
| Windows Binary (x86_64) | spicyR_1.99.6.zip |
| macOS Binary (big-sur-x86_64) | spicyR_1.99.6.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/spicyR/ |
| Package Short Url | https://bioconductor.org/packages/spicyR/ |
| Package Downloads Report | Download Stats |