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
- Dionysus A persistence library kept for what the fast Rips engines do not do — vineyards, zigzag, and persistence over arbitrary fields. Package
- 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-ph A parallel Vietoris–Rips persistence engine that gathers three separate lines of Ripser work into one implementation. Package
- giotto-tda giotto-tda, the scikit-learn-compatible TDA toolkit, and the corpus's deliberate out-of-profile L0 fixture. Environment
- giotto-tda The scikit-learn-shaped TDA toolkit at the head of the Giotto family — and the corpus's clearest case of a license that constrains how software may be served. Package
- gudhi GUDHI, the general-purpose computational topology library covering simplicial complexes, filtrations, and persistence. Environment
- GUDHI The broadest general-purpose computational topology library, and the one whose effective license depends on which of its modules you use. Package
- KeplerMapper The scikit-tda implementation of Mapper — cover, cluster, take the nerve — producing an inspectable graph rather than a barcode. Package
- 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
- persim The scikit-tda representation layer — distances between persistence diagrams, and the vectorizations that turn one into a fixed-length feature. Package
- 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
- pyDowker Persistence from a relation instead of a metric — a rectangular incidence matrix can be filtered where a distance matrix is required elsewhere. Package
- pyrivet The pure-Python interface to RIVET — trivial to build, and useless without the console engine the sibling recipe supplies. Recipe
- pyrivet The Python interface to RIVET — it builds bifiltrations and shells out to the console engine, which is why it can install perfectly and compute nothing. Package
- 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 The lean C++ engine that made Vietoris-Rips persistence fast enough to stop being the bottleneck, in about a thousand lines. Package
- 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
- ripser.py The scikit-tda Python interface over the Ripser engine, returning persistence diagrams as arrays a scripted analysis can use. Package
- 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
- RIVET The reference tool for two-parameter persistence — it answers by letting you interrogate the module, because there is no barcode to hand you. Package
- 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
- scikit-tda The umbrella package for the Python TDA stack — it implements nothing, and asserts that its members work together. Package
- 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
- tadasets Synthetic point clouds whose homology is known in advance — the shapes a TDA implementation is checked against. Package