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A R source repository on GitHub. It provides functions for processing the outputs of Anchor to build machine learning models, and otherwise process and visualize the data.

What belongs in the repository?


Package Description
anchor-r General utility functions for interacting with Anchor output.
anchor-r-features Processing feature-export data (CSV) from Anchor (building classifiers, plotting etc.)
anchor-r-experiment Class for accessing the structured output from an Anchor experiment.
anchor-r-nuclei Functions to help with nuclei segmentation pipelines.

Code structure

  • Each function is documented in its header (in the respective R/ subdirectory).
  • The NAMESPACE file specifies which functions are publicly-exposed.
  • R-package dependencies are listed in the DESCRIPTION file and in NAMESPACE.


Before using these functions in a script elsewhere, a package must be installed locally, either:

  • Use RStudio, open each project, and select the Build & Reload button in the Build panel in the top-right, or
  • Use the make script (make.bat/ make.sh) in the packages’s top-level folder (after first adding your R executable to the system path).