Cluster Analysis Python Packages

hdbscan

A high performance implementation of HDBSCAN clustering.

quitefastmst

quitefastmst: Euclidean and Mutual Reachability Minimum Spanning Trees

lumbermark

Lumbermark: Resistant Clustering via Chopping Up Mutual Reachability Minimum Spanning Trees

sequenzo

A fast, scalable, and intuitive Python package in sequence analysis.

genieclust

Genie: Fast and Robust Hierarchical Clustering

pytomato

A pure-Python implementation of the ToMATo clustering algorithm.

persistable-clustering

density-based clustering for exploratory data analysis based on multi-parameter persistence

pyclustertend

A python package to assess cluster tendency

s-dbw

S_Dbw validity index. Adapted for DBSCAN (and similar)

compsil

CompSil: Composite Silhouette for Cluster-Count Selection

hdbscan-314

A high performance implementation of HDBSCAN clustering.

bf44-hdbscan-0844

A high performance implementation of HDBSCAN clustering.

finchpy

A Python implementation of "FINCH Clustering Algorithm (CVPR 2019)"

gpmix

A library for efficient uncovering of latent cluster labels in functional data from Gaussian process mixtures.

clustering-benchmarks

A Framework for Benchmarking Clustering Algorithms

biocluster

Biocluster analyzes Pareto-front solutions from multi-objective gene clustering: builds consensus partitions, computes GO semantic similarity, flags structurally vs. biologically discrepant solutions, and generates interactive heatmaps, enrichment plots and GO networks.

clusterking

Cluster sets of histograms/curves, in particular kinematic distributions in high energy physics.

cake-ensemble

Confidence in Assignments via K-partition Ensembles

hopkins-statistic

A Python package for computing the Hopkins statistic to assess clustering tendency.

trcc

Density-peak clustering with path-density mutual-reachability merging. Sub-quadratic O(n log n) via a C++ pybind11/nanoflann kd-tree. 30× speedup at n=50k.

edtools

Collection of tools for automated processing and clustering of electron diffraction data

cluster-ss

Python cluster-ss Package

extclustval

A lightweight Python package for external clustering validation metrics.

composite-silhouette

A clustering evaluation framework that combines micro- and macro-averaged silhouette scores into a composite metric using statistical weighting.