spicyR
This is thereleased version of spicyR; for the devel version, seespicyR.
Spatial analysis of in situ cytometry data
Bioconductor version: Release (3.22)
The spicyR package provides a framework for performing inference on changes in spatial relationships between pairs of cell types for cell-resolution spatial omics technologies. spicyR consists of three primary steps: (i) summarizing the degree of spatial localization between pairs of cell types for each image; (ii) modelling the variability in localization summary statistics as a function of cell counts and (iii) testing for changes in spatial localizations associated with a response variable.
Author: Nicolas Canete [aut], Ellis Patrick [aut, cre], Nicholas Robertson [ctb], Alex Qin [ctb], Farhan Ameen [ctb], Shreya Rao [ctb]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("spicyR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("spicyR")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("spicyR")| Spatial Linear and Mixed-Effects Modelling with spicy | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays,SingleCell,Software,Spatial |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.1) |
| Imports | BiocParallel,ClassifyR,S4Vectors,SingleCellExperiment,SpatialExperiment,SummarizedExperiment,cli,concaveman,coxme,data.table,dplyr,ggforce,ggh4x,ggnewscale,ggplot2,ggthemes, grDevices,lifecycle,lmerTest,magrittr, methods,pheatmap,rlang,scales,scam,simpleSeg,spatstat.explore,spatstat.geom, stats,survival,tibble,tidyr |
| System Requirements | |
| URL | https://ellispatrick.github.io/spicyR/https://github.com/SydneyBioX/spicyRhttps://sydneybiox.github.io/spicyR/ |
| Bug Reports | https://github.com/SydneyBioX/spicyR/issues |
See More
| Suggests | SpatialDatasets,BiocStyle,knitr,rmarkdown,pkgdown,imcRtools,testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | lisaClust, OSTA |
| Suggests Me | Statial,spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | spicyR_1.22.0.tar.gz |
| Windows Binary (x86_64) | spicyR_1.22.0.zip (64-bit only) |
| macOS Binary (x86_64) | spicyR_1.22.0.tgz |
| macOS Binary (arm64) | spicyR_1.22.0.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 |