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
exploring-cybersecurity-data-science
Exploring Cybersecurity Data Science: Dimensionality Reduction and Cluster Analysis
ru-resilient-arctic-clusters
This repository contains some supplementary materials (code, data and plots) for the paper “Resilience Potential of the Russian Arctic Cities".
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)
slisemap
SLISEMAP: Combining supervised dimensionality reduction with local explanations
mafese
Feature Selection using Metaheuristics Made Easy: Open Source MAFESE Library in Python
evolution-paths
Visualizing Runtime Evolution Paths in a Multidimensional Space
https://github.com/arvkevi/ezancestry
Easy genetic ancestry predictions in Python
tsimcne
Unsupervised visualization of image datasets using contrastive learning
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.
ml-oneday-course
This is a one-day machine learning introductory course for beginners
DiRe - JAX
DiRe - JAX: A JAX based Dimensionality Reduction Algorithm for Large-scale Data - Published in JOSS (2025)
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)
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)
https://github.com/polis-community/red-dwarf
A DIMensional REDuction library for reproducing and experimenting with Polis-like data pipelines.
ridgetorus
PCA on the torus using density ridges. Software companion for "Toroidal PCA via density ridges"
nplstoolbox
Creation and selection of N-way Partial Least Squares (NPLS) models
scdownstream
A single cell transcriptomics pipeline for QC, integration and making the data presentable