Introduction to Topological Data Analysis
- TDA describes data forms.
- Betti numbers allows us to find conected components and 1-holes in data sets.
Computational Tools for TDA
- GUDHI is a TDA tool
- GUDHI uses simplextree objects to efficiently store simplicial complexes
- GUDHI allows creating simplicial complexes from datasets, distance matrices, simulated data, and manually
Detecting horizontal gene transfer
- Horizontal Gene Transfer (HGT) is a phenomenon where an organism transfers genetic material to another one that is not its descendant.
- 1-holes can detect HGT.
Persistence Simplices gives rise to Gene Families
- Pangenomes can be described using TDA
- Persistence simplices are related to the gene families of a Pangenome
- Persistence simplices can be used to find some funtional families
Other Resources
- Giotto-TDA and tdaverse are other resources to learn TDA