For a recent comparison of persistence software, see Nina Otter et al., “A roadmap for the computation of persistent homology”.
Mapper
- Slides about Mapper by Matthew Wright
- Notes on TDA Mapper by Lori Ziegelmeier
- Original mapper paper: Singh, Memoli, Carlsson, “Topological Methods for the Analysis of High Dimensional Data Sets and 3D Object Recognition”
- R package: TDA Mapper
- Data analysis startup based on the Mapper algorithm: Ayasdi
Macaulay2
- To open Macaulay2 in the Macalaster lab, open a Terminal and type /Applications/Macaulay2-1.9.2/bin/M2
- Macaulay2 Notes by Lori Ziegelmeier
- Try Macaulay2 in your browser
Javaplex
- Javaplex examples by Lori Ziegelmeier
- Javaplex Github page: https://github.com/appliedtopology/javaplex
- Javaplex tutorial by Henry Adams and Andrew Tausz
- Zig-zag examples by Lori Ziegelmeier
Ripser
- Fast, in-browser persistent homology computation: live.ripser.org
- Ripser Github page: https://github.com/Ripser/ripser
- Slides about Ripser by Ulrich Bauer
R TDA Package
- R TDA demonstration by Matthew Wright
- R TDA tutorial by Mathieu Carrière and Steve Oudot
- Paper: Introduction to the R package TDA
- Package documentation: CRAN page, Reference manual
GUDHI
- GUDHI library website: gudhi.gforge.inria.fr
- Documentation
- Download: Source code and precompiled files
- Experiments: Sample data and instructions to experiment with GUDHI
RIVET
- RIVET slides by Matthew Wright
- Project web site: http://rivet.online
- RIVET Github page: https://github.com/rivetTDA/rivet
- Paper: Lesnick and Wright, “Interactive Visualization of 2-D Persistence Modules”