phenoptr contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences’ inForm® software.
phenoptr is part of the Akoya Biosciences Phenoptics™ family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.
phenoptr from GitHub. In the RStudio console, copy and paste or type these commands (press Enter after each line):
install.packages("devtools") devtools::install_github("akoyabio/phenoptr", build_vignettes=TRUE)
When requested, enter
1 (Yes) to install BiocInstaller.
These Tutorials introduce the most important features of
phenoptr’s spatial processing capabilities—finding nearest neighbor distances, counting cells within a radius, and visualizing nearest neighbors.
R is a powerful and popular environment for data manipulation and statistical analysis. Many learning resources are available online.
phenoptr is designed to work in harmony with packages in the tidyverse.
data_frame) is the preferred representation of tabular data.
If you’d like to learn more about the tidyverse packages, a good place to start is Garrett Grolemund and Hadley Wickham’s book, available free online at R for data science. If you are new to R, the book’s Introduction will help you get started.