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topolow v0.1.0
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@omid-arhami omid-arhami released this 06 Feb 22:48
· 17 commits to main since this release
v0.1.0
5bb9041

TopoLow v0.1.0

First public release of the TopoLow algorithm for antigenic cartography mapping and analysis. This version implements a physics-inspired approach combining spring forces and repulsive interactions to optimize point configurations in high-dimensional spaces.

Key Features

  • Core optimization algorithm with configurable parameters
  • Support for both SLURM clusters and local machines (Windows/Unix)
  • Handling of missing and thresholded measurements
  • Interactive visualization tools
  • Cross-validation and error analysis capabilities
  • Network structure analysis
  • Comprehensive test coverage and validation

Installation

Windows users should use the .zip binary, while Unix/Mac users can install from the .tar.gz source package. For direct installation from GitHub:

devtools::install_github("omid-arhami/topolow")

Documentation

Full documentation is available within the package:

library(topolow)
?topolow

Validation

All functions and methodologies have been extensively tested and validated as described in the paper. If you use Topolow, please cite:
TOPOLOW: A MAPPING ALGORITHM FOR ANTIGENIC CROSS-REACTIVITY AND BINDING AFFINITY ASSAY RESULTS
Omid Arhami, Pejman Rohani
bioRxiv 2025.02.09.637307; doi: https://doi.org/10.1101/2025.02.09.637307
(under peer review)

Notes

  • Requires R ≥ 4.1.0
  • SLURM functionality is available and only needed for cluster computing for large-scale problems

Bug Reports

Please report any issues at: https://github.com/omid-arhami/topolow/issues

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