Umap Python Packages

umap-learn

Uniform Manifold Approximation and Projection

torchdr

TorchDR - PyTorch Dimensionality Reduction

protspace

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

protlabel

Explore protein language model embeddings in your browser — surface relationships sequence similarity misses, overlay annotations, and transfer labels (EAT). Nothing uploaded.

manifolds-rs

Various embedding methods such as UMAP, tSNE, diffusion maps etc. implemented in Rust. Now with Python bindings

metalcyte

Fast single-cell RNA-seq analysis on Apple silicon Macs, with a Rust engine, Metal GPU kernels and support for datasets larger than memory

mepylome

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

ilayoutx

Graph layout algorithms in Rust/Python

openflo

Openflo: a open source flow cytometry repo with flowjo compatibility and automation pipeline

imbed

Tools to work with embeddings

ellama

Embeddings interface for Ollama

oversampleqa

A question-answering project focused on handling imbalanced datasets through advanced oversampling techniques.

phenotopo

A QC and explainability toolkit for phenotype cohorts: HPO/Phenopacket quality control, annotation-bias checks, outliers, ontology-aware group comparison and robust cohort structure.

simpletopicmodel

Easily identifying themes in text

mlx-vis

Pure MLX implementations of UMAP, t-SNE, PaCMAP, TriMap, DREAMS, CNE, MMAE, and NNDescent for Apple Silicon. Metal GPU for computation and video rendering.

dire-rapids

DiRe accelerated by PyTorch, PyKeOps and cuVS

umato

Uniform Manifold Approximation with Two-phase Optimization (IEEE VIS 2022 short)

dire-jax

DImensionality REduction in JAX

dbmap

Deprecated in favour of TopoMetry: https://github.com/davisidarta/topometry

lakshana

Zero-config schema discovery for document collections. Drop a folder of PDFs, get a JSON Schema.

knrscore

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

lensed-umap

Functions that filter UMAP graphs using domain knowledge.

umapjax

UMAP, but accelerated.

usum

USUM: Plotting sequence similarity using USEARCH & UMAP & t-SNE