dimension-reduction

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

bioinformatics big-data genomics clustering scrna-seq graph-analytics memory-efficient tsne differential-expression umap dimension-reduction single-cell-genomics single-cell-rna-seq scalable-data-analysis single-cell-atac-seq multiomics cite-seq pseudotime scatac-seq gene-modules

UpdatedNov 19, 2025
Python

erichson /rSVD

Star102

Randomized Matrix Decompositions using R

cran pca svd principal-component-analysis dimension-reduction singular-value-decomposition randomized-algorithm matrix-approximation probabilistic-algorithms

UpdatedApr 13, 2021
R

BallisticLA /RandBLAS

Star96

A header-only C++ library for sketching in randomized linear algebra

linear-algebra sketching dimension-reduction numerical-linear-algebra

UpdatedFeb 4, 2026
C++

katiana22 /latent-deeponet

Star77

Source code of "Learning nonlinear operators in latent spaces for real-time predictions of complex dynamics in physical systems."

regression partial-differential-equations materials-science fluid-dynamics dimension-reduction latent-spaces deeponet neural-operators

UpdatedApr 24, 2025
Python

erichson /spca

Star71

Sparse Principal Component Analysis (SPCA) using Variable Projection

pca dimensionality-reduction dimension-reduction spca

UpdatedApr 7, 2018
R

davpinto /fastknn

Star70

Fast k-Nearest Neighbors Classifier for Large Datasets

kaggle feature-extraction rstats nearest-neighbors feature-engineering knn decision-boundaries shrinkage-estimator dimension-reduction

UpdatedSep 17, 2017
R

kisungyou /Rdimtools

Star55

Dimension Reduction and Estimation Methods

r manifold-learning dimension-reduction subspace-learning dimension-estimation

UpdatedSep 22, 2025
R

derohde /Fred

Star51

A fast, scalable and light-weight C++ Fréchet and DTW distance library, exposed to python and focused on clustering of polygonal curves.

python algorithm time-series clustering trajectory-analysis dynamic-time-warping dimension-reduction trajectory distance-calculation frechet-distance sequential-data trajectory-clustering fr-chet-distance frechet polygonal-chain continuous-frechet-distance dimensional-polygonal-curves nearest-centers sampling-algorithms polygonal-curves

UpdatedAug 29, 2023
C++

hippylib /hippyflow

Star39

Dimension reduced surrogate construction for parametric PDE maps

deep-learning neural-networks dimensionality-reduction reduced-basis dimension-reduction proper-orthogonal-decomposition surrogate-models reduced-order-surrogate-model active-subspace karhunen-loeve reduced-order-modeling parametric-pde parametric-pdes

UpdatedAug 26, 2025
Python

milescsmith /ReductionWrappers

Star36

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

python wrapper bioinformatics dimensionality-reduction tsne forceatlas2 umap dimension-reduction force-directed-graphs wrappers seurat singlecellexperiment singlecellexperiment-objects paga phate opentsne pacmap dimensional-reduction

UpdatedDec 30, 2024
R

Geometric Dynamic Variational Autoencoders (GD-VAEs) for learning embedding maps for nonlinear dynamics into general latent spaces. This includes methods for standard latent spaces or manifold latent spaces with specified geometry and topology. The manifold latent spaces can be based on analytic expressions or general point cloud representations.

machine-learning deep-learning point-cloud neural-networks dynamical-systems manifold-learning dimension-reduction geometric-algorithms topological-data-analysis variational-autoencoder parameterized-systems geometric-deep-learning pytorch-implementation autoencoder-neural-network latent-spaces