OOMPA PROJECT
Cytangle
The Cytangle R-Forge project is one component of the broader OOMPA Project produced by the Coombes Lab over the past decade-plus.List of Packages
- RPointCloud
- Visualizing Topological Loops and Voids Visualizations to explain the results of a topological data analysis. The goal of topological data analysis is to identify persistent topological structures, such as loops (topological circles) and voids (topological spheres), in data sets. The output of an analysis using the 'TDA' package is a Rips diagram (named after the mathematician Eliyahu Rips). The goal of 'RPointCloud' is to fill in these holes in the data by providing tools to visualize the features that help explain the structures found in the Rips diagram. See McGee and colleagues (2024) and (2026).
- WayFindR
- Computing Graph Structures on WikiPathways Converts pathways from 'WikiPathways' GPML format or 'KEGG' KGML format into 'igraph' objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition). See the manuscript by Bombina and colleagues.
- EBGLIDE
- Testing Significance of Topological Loops and Voids The method of topological data analysis uses persistent homology to discover intersting toplogical structurs (includig loops and voids) from "point cloud" data sets. One of the statistical challenges is to distinguish transient noise from long-lasting biologically meaningful structure. EBGLIDE provides tools to help solve this problem. Under Development
- Cytangle
- Analyzing Single Cell Mass Cytometry Data Defines classes and methods to analyze how relationships between protein markers vary in single cell mass cytometry data. Under Development
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