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.
phenoptrfrom GitHub. In the RStudio console, copy and paste or type these commands (press Enter after each line):
1(Yes) to install BiocInstaller.
Two optional packages are recommended in specific circumstances.
tiffpackage includes support for tiled images and allows
phenoptrto work with 2x2 component images from inForm. See the installation instructions in the package README file.
rtreepackage dramatically speeds calculation and reduces memory requirements of spatial metrics such as nearest neighbors and count within. See the installation instructions in the package README file.
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.