spicyR
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see spicyR.
Spatial analysis of in situ cytometry data
Bioconductor version: 3.13
spicyR provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.
Author: Nicolas Canete [aut], Ellis Patrick [aut, cre]
Maintainer: Ellis Patrick <ellis.patrick at sydney.edu.au>
citation("spicyR")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 SegmentedCells | HTML | R Script |
| Introduction to spicy | HTML | R Script |
| Reference Manual |
Details
| biocViews | CellBasedAssays, SingleCell, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | GPL (>=2) |
| Depends | R (>= 4.0.0) |
| Imports | ggplot2, concaveman, BiocParallel, spatstat.core, spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats, data.table, dplyr, tidyr |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/ellispatrick/spicyR/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | lisaClust |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spicyR_1.4.0.tar.gz |
| Windows Binary | spicyR_1.4.0.zip |
| macOS 10.13 (High Sierra) | spicyR_1.4.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |