UMAP
UMAP: Uniform Manifold Approximation and Projection - Published in JOSS (2018)
partition
partition: A fast and flexible framework for data reduction in R - Published in JOSS (2020)
scPCA
scPCA: A toolbox for sparse contrastive principal component analysis in R - Published in JOSS (2020)
ivis
ivis: dimensionality reduction in very large datasets using Siamese Networks - Published in JOSS (2019)
lfda
lfda: Local Fisher Discriminant Analysis in R - Published in JOSS (2019)
dml
dml: Distance Metric Learning in R - Published in JOSS (2018)
fABBA
fABBA: A Python library for the fast symbolic approximation of time series - Published in JOSS (2024)
ExpFamilyPCA.jl
ExpFamilyPCA.jl: A Julia Package for Exponential Family Principal Component Analysis - Published in JOSS (2025)
DREiMac
DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates - Published in JOSS (2023)
t-elf
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.
xeofs
xeofs: Comprehensive EOF analysis in Python with xarray - Published in JOSS (2024)
spilterlize_integrate
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.
minisom
:red_circle: MiniSom is a minimalistic implementation of the Self Organizing Maps
vmrseq
An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models.
knrscore
KNRScore is a Python package for computing K-Nearest-Rank Similarity, a metric that quantifies local structural similarity between two maps or embeddings.
unsupervised_analysis
A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.
msmbuilder
:building_construction: Statistical models for biomolecular dynamics :building_construction:
dpca
An implementation of demixed Principal Component Analysis (a supervised linear dimensionality reduction technique)
r-sparsepca
Sparse Principal Component Analysis (SPCA) using Variable Projection
ru-resilient-arctic-clusters
This repository contains some supplementary materials (code, data and plots) for the paper “Resilience Potential of the Russian Arctic Cities".
scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable
DiRe - JAX
DiRe - JAX: A JAX based Dimensionality Reduction Algorithm for Large-scale Data - Published in JOSS (2025)
https://github.com/arvkevi/ezancestry
Easy genetic ancestry predictions in Python
ridgetorus
PCA on the torus using density ridges. Software companion for "Toroidal PCA via density ridges"
mafese
Feature Selection using Metaheuristics Made Easy: Open Source MAFESE Library in Python
slisemap
SLISEMAP: Combining supervised dimensionality reduction with local explanations
parafac4microbiome
Creation and selection of Parallel Factor Analysis models of longitudinal microbiome data.
pcpr
An R package implementing Principal Component Pursuit for pattern recognition in environmental health.
evolution-paths
Visualizing Runtime Evolution Paths in a Multidimensional Space
ml-oneday-course
This is a one-day machine learning introductory course for beginners
https://github.com/polis-community/red-dwarf
A DIMensional REDuction library for reproducing and experimenting with Polis-like data pipelines.
OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis
OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis - Published in JOSS (2026)
OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization
OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - Published in JOSS (2026)
nplstoolbox
Creation and selection of N-way Partial Least Squares (NPLS) models
tsimcne
Unsupervised visualization of image datasets using contrastive learning
exploring-cybersecurity-data-science
Exploring Cybersecurity Data Science: Dimensionality Reduction and Cluster Analysis
https://github.com/berenslab/umi-normalization
Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology
CompressedBeliefMDPs.jl
CompressedBeliefMDPs.jl: A Julia Package for Solving Large POMDPs with Belief Compression - Published in JOSS (2025)