Top 13 umap open source projects

Uniform Manifold Approximation and Projection

✭ 5,268

python machine-learning visualization dimensionality-reduction umap topological-data-analysis

Workshop (6 hours): Clustering (Hdbscan, LCA, Hopach), dimension reduction (UMAP, GLRM), and anomaly detection (isolation forests).

✭ 34

r clustering dimensionality-reduction unsupervised-learning umap hdbscan isolation-forests glrm latent-class-analysis

dbMAP

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

✭ 39

python visualization machine-learning dimensionality-reduction nearest-neighbors single-cell graph-layout umap diffusion-process denoising high-dimensional

UMAP.jl

Uniform Manifold Approximation and Projection (UMAP) implementation in Julia

✭ 93

julia Jupyter Notebook visualization machine-learning dimensionality-reduction umap topological-data-analysis

Embeddings2Image

create "Karpathy's style" 2d images out of your image embeddings

✭ 52

python visualization tsne umap

ReductionWrappers

R wrappers to connect Python dimensional reduction tools and single cell data objects (Seurat, SingleCellExperiment, etc...)

✭ 31

r wrapper bioinformatics dimensionality-reduction tsne forceatlas2 umap dimension-reduction force-directed-graphs wrappers seurat singlecellexperiment singlecellexperiment-objects paga phate opentsne pacmap dimensional-reduction

Interactive-3D-Plotting-in-Seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

✭ 80

r plotting rna-seq-analysis umap scrnaseq seurat 3dtsne 3dpca 3dumap scrnaseq-data seurat-objects

umap-java

A Uniform Manifold Approximation and Projection (UMAP) library for Java, developed by Tag.bio in collaboration with Real Time Genomics.

✭ 16

java algorithms umap tagbio realtimegenomics

AnnA Anki neuronal Appendix

Using machine learning on your anki collection to enhance the scheduling via semantic clustering and semantic similarity

✭ 39

python nlp ai flashcards clustering scheduler pca machinelearning kmeans anki embedding doc2vec bert umap latent sentence-embeddings neighbourhood sbert sementics

playing with vae

Comparing FC VAE / FCN VAE / PCA / UMAP on MNIST / FMNIST

✭ 53

Jupyter Notebook python tutorial pytorch mnist pca beginner embedding umap variational-autoencoder fashion-mnist

BEER

BEER: Batch EffEct Remover for single-cell data

✭ 19

r python scrna-seq umap batch-effects single-cell-analysis scatac-seq

ParametricUMAP paper

Parametric UMAP embeddings for representation and semisupervised learning. From the paper "Parametric UMAP: learning embeddings with deep neural networks for representation and semi-supervised learning" (Sainburg, McInnes, Gentner, 2020).

✭ 132

Jupyter Notebook python machine-learning dimensionality-reduction representation-learning umap semisupervised-learning

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

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