Modality
modality/point-cloud
Generic point clouds and distance matrices, without a fixed biological source.
Notes
- dionysus Dionysus, a persistent-homology library with support for vineyards and circular coordinates alongside ordinary persistence. Environment
- giotto-ph The parallel Ripser-derived persistence backend, built from git because it vendors its C++ engine as submodules an sdist cannot carry. Recipe
- giotto-ph giotto-ph, a parallel Rips persistence backend, built from an in-repo recipe because it vendors its C++ engine as submodules. Environment
- giotto-tda giotto-tda, the scikit-learn-compatible TDA toolkit, and the corpus's deliberate out-of-profile L0 fixture. Environment
- gudhi GUDHI, the general-purpose computational topology library covering simplicial complexes, filtrations, and persistence. Environment
- kmapper KeplerMapper's implementation of the Mapper algorithm, packaged here because a pure-Python library on PyPI is on no conda channel. Recipe
- kmapper KeplerMapper, a Python implementation of the Mapper algorithm for building nerve-graph summaries of a point cloud. Environment
- Mapper Compress a dataset into a graph by covering the range of a chosen filter function and clustering within each piece. Method
- Multiparameter Persistence Filter along two parameters at once — scale and density, say — when one axis cannot separate structure from noise. Method
- Persistent Homology Track holes across every scale at once instead of picking one, and record where each appears and dies. Method
- Persistent Spectral Graph The founding persistent-Laplacian paper: harmonic spectra recover persistent homology exactly, and non-harmonic spectra carry the geometry it discards. Paper
- Persistent Topological Laplacians A Laplacian family built along a filtration; its zero eigenvalues are persistent homology, and the rest are the geometry persistence throws away. Method
- PETLS A C++ library with Python bindings for building persistent topological Laplacians and computing their matrices and spectra. Package
- pydowker Dowker complexes from arbitrary relations, and the leaf of a three-recipe chain that was a hollow green until the engine underneath it existed. Recipe
- pydowker The full two-parameter persistence stack: pyDowker over pyrivet over the RIVET console engine, built as a three-recipe chain. Environment
- pyrivet The pure-Python interface to RIVET — trivial to build, and useless without the console engine the sibling recipe supplies. Recipe
- r-tda The established general-purpose R package for the field, packaged from CRAN with a compiled dependency set that is still a best guess. Recipe
- r-tda The R TDA package, covering persistent homology, density clustering, and statistical inference on diagrams from R. Environment
- r-tdastats The Ripser-backed R persistence package, built from CRAN because no conda channel carries the R side of the field at all. Recipe
- r-tdastats TDAstats, a lightweight R interface to Ripser with plotting and hypothesis testing on persistence diagrams. Environment
- ripser-cpp The Ripser C++ command-line tool for fast Vietoris-Rips persistent homology, installed as a single Bioconda package. Environment
- ripser-py The ripser.py Python bindings over the Ripser engine, for computing persistence diagrams inside a Python workflow. Environment
- rivet RIVET's Qt-free console engine for two-parameter persistence, compiled from a pinned master commit and deliberately published under a different package name. Recipe
- scikit-tda The meta-package that pulls the Python TDA stack together behind one install, built here because the channels carry the parts but not the whole. Recipe
- scikit-tda The scikit-tda meta-package, pulling the Python TDA stack together behind one install. Environment
- Spectral Geometry Recover a dataset's latent geometry from the spectrum of an operator built on its neighbourhood graph, rather than assuming a shape in advance. Method
- tadasets The scikit-tda synthetic-dataset generator, and the only recipe here with a pull request open against a public channel. Recipe