README.md

In milescsmith/ReductionWrappers: Wrapper exposing several Python dimensional reduction tools

ReductionWrappers

R wrappers around dimensionality reduction methods found in Python modules. Uses the reticulate package to expose functionality. Additionally provides bridging functions that let these work as drop-in replacements when working with Seurat (verions 3) and SingleCellExperiment objects. Currently wraps: * ForceAtlas2, using the Python implementation found here. Currently works for Seurat objects only (and will remain so until I can find a fast algorithm for computing simultaneous nearest neighbors for SingleCellExperiment objects). * openTSNE * UMAP (Uniform Manifold Approximation and Projection) * PaCMAP (Pairwise Controlled Manifold Approximation) * PAGA (Partition-Based Graph Abstraction) through Scanpy. * PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding) * PhenoGraph

milescsmith/ReductionWrappers documentation built on March 25, 2023, 11:58 a.m.