Scientific Software
Updated 6 months ago

UMAP — Peer-reviewed • Rank 29.1 • Science 95%

UMAP: Uniform Manifold Approximation and Projection - Published in JOSS (2018)

Engineering (40%) Materials Science (40%)
Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

partition — Peer-reviewed • Rank 10.8 • Science 98%

partition: A fast and flexible framework for data reduction in R - Published in JOSS (2020)

Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

scPCA — Peer-reviewed • Rank 13.7 • Science 95%

scPCA: A toolbox for sparse contrastive principal component analysis in R - Published in JOSS (2020)

Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

ivis — Peer-reviewed • Rank 14.7 • Science 93%

ivis: dimensionality reduction in very large datasets using Siamese Networks - Published in JOSS (2019)

Biochemistry, Genetics and Molecular Biology
Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

lfda — Peer-reviewed • Rank 12.7 • Science 93%

lfda: Local Fisher Discriminant Analysis in R - Published in JOSS (2019)

Scientific Software
Updated 6 months ago

dml — Peer-reviewed • Rank 12.3 • Science 93%

dml: Distance Metric Learning in R - Published in JOSS (2018)

Scientific Software
Updated 6 months ago

fABBA — Peer-reviewed • Rank 10.2 • Science 95%

fABBA: A Python library for the fast symbolic approximation of time series - Published in JOSS (2024)

Scientific Software
Updated 6 months ago

ExpFamilyPCA.jl — Peer-reviewed • Rank 4.5 • Science 100%

ExpFamilyPCA.jl: A Julia Package for Exponential Family Principal Component Analysis - Published in JOSS (2025)

Scientific Software
Updated 6 months ago

DREiMac — Peer-reviewed • Rank 9.7 • Science 93%

DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates - Published in JOSS (2023)

Mathematics
Scientific Software · Peer-reviewed
Updated 6 months ago

t-elf • Rank 5.5 • Science 85%

Tensor Extraction of Latent Features (T-ELF). Within T-ELF's arsenal are non-negative matrix and tensor factorization solutions, equipped with automatic model determination (also known as the estimation of latent factors - rank) for accurate data modeling. Our software suite encompasses cutting-edge data pre-processing and post-processing modules.

Updated 6 months ago

chemplot • Rank 11.7 • Science 77%

A python package for chemical space visualization.

Scientific Software
Updated 6 months ago

xeofs — Peer-reviewed • Rank 14.9 • Science 67%

xeofs: Comprehensive EOF analysis in Python with xarray - Published in JOSS (2024)

Mathematics Artificial Intelligence and Machine Learning Engineering
Scientific Software · Peer-reviewed
Updated 6 months ago

opentsne • Rank 20.4 • Science 59%

Extensible, parallel implementations of t-SNE

Updated 6 months ago

spilterlize_integrate • Rank 3.9 • Science 67%

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

Updated 6 months ago

uwot • Rank 20.3 • Science 46%

An R package implementing the UMAP dimensionality reduction method.

Updated 6 months ago

vmrseq • Rank 10.9 • Science 49%

An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models.

Updated 6 months ago

knrscore • Rank 4.9 • Science 54%

KNRScore is a Python package for computing K-Nearest-Rank Similarity, a metric that quantifies local structural similarity between two maps or embeddings.

Updated 6 months ago

destiny • Rank 19.2 • Science 36%

R package for single cell and other data analysis using diffusion maps

Updated 6 months ago

unsupervised_analysis • Rank 4.7 • Science 49%

A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

Updated 6 months ago

umap • Rank 17.1 • Science 23%

Uniform Manifold Approximation and Projection - R package

Updated 6 months ago

ReducedExperiment • Rank 8.9 • Science 26%

Containers and tools for dimensionally-reduced -omics data

Updated 6 months ago

msmbuilder • Rank 14.4 • Science 20%

:building_construction: Statistical models for biomolecular dynamics :building_construction:

Updated 6 months ago

dpca • Rank 14.0 • Science 20%

An implementation of demixed Principal Component Analysis (a supervised linear dimensionality reduction technique)

Updated 6 months ago

r-sparsepca • Rank 13.1 • Science 20%

Sparse Principal Component Analysis (SPCA) using Variable Projection

Updated 6 months ago

ru-resilient-arctic-clusters • Science 54%

This repository contains some supplementary materials (code, data and plots) for the paper “Resilience Potential of the Russian Arctic Cities".

Updated 6 months ago

scdownstream • Science 57%

A single cell transcriptomics pipeline for QC, integration and making the data presentable

Updated 6 months ago

booklet • Science 26%

Multivariate exploratory data analysis in R

Scientific Software
Updated 6 months ago

DiRe - JAX — Peer-reviewed • Science 93%

DiRe - JAX: A JAX based Dimensionality Reduction Algorithm for Large-scale Data - Published in JOSS (2025)

Updated 6 months ago

ridgetorus • Science 13%

PCA on the torus using density ridges. Software companion for "Toroidal PCA via density ridges"

Updated 6 months ago

parafac4microbiome • Science 49%

Creation and selection of Parallel Factor Analysis models of longitudinal microbiome data.

Updated 6 months ago

pcpr • Science 13%

An R package implementing Principal Component Pursuit for pattern recognition in environmental health.

Updated 6 months ago

nif • Science 36%

A library for dimensionality reduction on spatial-temporal PDE

Updated 6 months ago

evolution-paths • Science 65%

Visualizing Runtime Evolution Paths in a Multidimensional Space

Updated 24 days ago

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis • Science 87%

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis - Published in JOSS (2026)

Updated 24 days ago

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization • Science 87%

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - Published in JOSS (2026)

Updated 6 months ago

trace • Science 67%

Interactive quality analysis for two-dimensional embeddings

Updated 6 months ago

nplstoolbox • Science 39%

Creation and selection of N-way Partial Least Squares (NPLS) models

Updated 6 months ago

exactodereduction.jl • Science 31%

Exact reduction of ODE models via linear transformations

Updated 6 months ago

tsimcne • Science 54%

Unsupervised visualization of image datasets using contrastive learning

Updated 6 months ago

https://github.com/berenslab/umi-normalization • Science 23%

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

Scientific Software
Updated 6 months ago

CompressedBeliefMDPs.jl — Peer-reviewed • Science 93%

CompressedBeliefMDPs.jl: A Julia Package for Solving Large POMDPs with Belief Compression - Published in JOSS (2025)