Packages - TDA Bioinformatics Foundry

TDA Bioinformatics Foundry

Dionysus A persistence library kept for what the fast Rips engines do not do — vineyards, zigzag, and persistence over arbitrary fields. method/persistent-homology modality/point-cloud
giotto-ph A parallel Vietoris–Rips persistence engine that gathers three separate lines of Ripser work into one implementation. method/persistent-homology modality/point-cloud
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. method/persistent-homology method/mapper modality/point-cloud
GUDHI The broadest general-purpose computational topology library, and the one whose effective license depends on which of its modules you use. method/persistent-homology modality/point-cloud
HiPoNet A multi-view simplicial complex network predicting cohort-level labels from high-dimensional cellular point clouds. method/simplicial-learning method/topological-deep-learning application/single-cell modality/high-dim-tabular
KeplerMapper The scikit-tda implementation of Mapper — cover, cluster, take the nerve — producing an inspectable graph rather than a barcode. method/mapper modality/point-cloud
open-topodockq-featurizer The MIT clean-room TopoDockQ interface featurizer, bit-exact against the bytecode-only original it replaces. method/persistent-laplacian application/structure-qa modality/molecular-structure
open-topoqa-featurizer The MIT clean-room TopoQA interface featurizer, written from the paper because the published implementation carries no license. method/persistent-homology application/structure-qa modality/molecular-structure
open-topoqa-scorer The MIT clean-room ProteinGAT interface-quality scorer, retrained from the paper rather than reusing an unlicensed checkpoint. method/topological-deep-learning application/structure-qa modality/molecular-structure
persim The scikit-tda representation layer — distances between persistence diagrams, and the vectorizations that turn one into a fixed-length feature. method/persistent-homology modality/point-cloud
PETLS A C++ library with Python bindings for building persistent topological Laplacians and computing their matrices and spectra. method/persistent-laplacian application/molecular-sciences modality/point-cloud modality/graph
petls-pytorch An Apache-2.0 PyTorch implementation of persistent topological Laplacians and the Foundry's shippable PETLS substitute. method/persistent-laplacian
PHAT The persistent-homology matrix-reduction backend — you bring the boundary matrix, it reduces it, and it lets you choose how. method/persistent-homology
pyDowker Persistence from a relation instead of a metric — a rectangular incidence matrix can be filtered where a distance matrix is required elsewhere. method/multiparameter-persistence method/persistent-homology modality/point-cloud
pyflagser Python bindings over the flagser engine, for persistence on directed flag complexes where edge orientation carries the signal. method/persistent-homology modality/graph
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. method/multiparameter-persistence modality/point-cloud
Ripser The lean C++ engine that made Vietoris-Rips persistence fast enough to stop being the bottleneck, in about a thousand lines. method/persistent-homology modality/point-cloud
ripser.py The scikit-tda Python interface over the Ripser engine, returning persistence diagrams as arrays a scripted analysis can use. method/persistent-homology modality/point-cloud
RIVET The reference tool for two-parameter persistence — it answers by letting you interrogate the module, because there is no barcode to hand you. method/multiparameter-persistence modality/point-cloud
scikit-tda The umbrella package for the Python TDA stack — it implements nothing, and asserts that its members work together. method/persistent-homology method/mapper modality/point-cloud
tadasets Synthetic point clouds whose homology is known in advance — the shapes a TDA implementation is checked against. method/persistent-homology modality/point-cloud
TopoDockQ A persistent-Laplacian scorer predicting DockQ interface quality to rank and filter peptide-protein docking poses. method/persistent-homology method/persistent-laplacian method/topological-deep-learning application/structure-qa modality/molecular-structure
TopoMetry An MIT-licensed toolkit for learning and evaluating spectral manifold representations of high-dimensional single-cell data. method/spectral-geometry application/single-cell modality/high-dim-tabular
TopoQA A topological deep learning model ranking predicted protein-complex structures by the quality of their interface. method/persistent-homology method/topological-deep-learning application/structure-qa modality/molecular-structure