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spicyR

Spatial analysis of in situ cytometry data.

Overview

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 such as high-definiton spatial transcriptomics.

Installation

For the Bioconductor release version, run the following.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("spicyR")

If you would like the most up-to-date features, install the most recent development version.

# Install the development version from Bioconductor:
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
# This will update all your Bioconductor packages to devel version
BiocManager::install(version='devel')

BiocManager::install("spicyR")

# Otherwise install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("ellispatrick/spicyR")
library(spicyR)

Submitting an issue or feature request

spicyR is still under active development. We would greatly appreciate any and all feedback related to the package.

  • R package related issues should be raised here.
  • For general questions and feedback, please contact us directly via [email protected].

Authors

Citation

Nicolas P Canete, Sourish S Iyengar, John T Ormerod, Heeva Baharlou, Andrew N Harman, Ellis Patrick, spicyR: spatial analysis of in situ cytometry data in R, Bioinformatics, Volume 38, Issue 11, 1 June 2022, Pages 3099–3105, https://doi.org/10.1093/bioinformatics/btac268