The PerkinElmer Phenoptics team is now part of Akoya Biosciences.
For the latest version of phenoptr
please visit https://akoyabio.github.io/phenoptr/. For information about
the acquisition, see this
press release.
phenoptr
contains functions that make it easier to read and analyze data tables
and images created by PerkinElmer's inForm® software.
phenoptr
is part of the PerkinElmer Phenoptics™ family of
Quantitative Pathology Research Solutions. For more information
visit the Phenoptics™
home page.
phenoptr
requires the R environment
for statistical computing, version 3.3.0 or higher. To install R,
visit the R download page.
The RStudio IDE
is highly recommended as well.
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("PerkinElmer/phenoptr", build_vignettes=TRUE)
1
(Yes) to install BiocInstaller.These Tutorials
introduce the most important features of phenoptr
.
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.
See the Reference section of the documentation for details on individual functions.
To cite package phenoptr
in publications use:
Kent S Johnson (2018). phenoptr: inForm Helper Functions. R package version 0.1.1.9007. https://perkinelmer.github.io/phenoptr/
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