Modality
modality/high-dim-tabular
High-dimensional feature matrices such as single-cell count data.
Notes
- ann-backends hnswlib and pynndescent together, pinning the approximate-nearest-neighbour backends that make kNN graphs reproducible. Environment
- batch-integration harmonypy and scanorama together, supplying the batch-integration step ahead of geometry learning on multi-sample cohorts. Environment
- hiponet The HiPoNet research codebase run from a pinned git clone, with a locked dependency closure but nothing installable to package. Environment
- HiPoNet A multi-view simplicial complex network predicting cohort-level labels from high-dimensional cellular point clouds. Package
- HiPoNet melanoma replication The closest recoverable released procedure reached 67.27% against a reported 90.90%, on a platform arm that cannot yet settle why. Replication experiment
- Mapper Compress a dataset into a graph by covering the range of a chosen filter function and clustering within each piece. Method
- phate PHATE, a diffusion-based embedding for visualizing continuous trajectory structure in single-cell data. Environment
- scanpy Scanpy and AnnData, the single-cell data structures and preprocessing the TopoMetry workflows are written against. Environment
- scvelo scVelo for RNA velocity, the velocity half of the cell-cycle replication, run downstream of the learned geometry. Environment
- scvi scvi-tools, the deep generative single-cell embedding used as a learned-representation comparator. 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
- topometry TopoMetry 1.1.0, built because conda-forge stops at a release that predates the API the eLife paper is written against. Recipe
- topometry TopoMetry 0.2.1.1 from conda-forge: a packaging fixture pinning the only build on the channel, four years behind the paper. Environment
- TopoMetry An MIT-licensed toolkit for learning and evaluating spectral manifold representations of high-dimensional single-cell data. Package
- TopoMetry cell-cycle replication The pancreas result reproduces directionally, but TopoMetry's 2-D layouts ignore their seed — so no single-run layout number should be quoted. Replication experiment
- topometry-1.1 TopoMetry 1.1.0, the release the eLife version of record describes, staged from an in-repo recipe that fixes two upstream defects. Environment