openTSNE: Extensible, parallel implementations of t-SNE

openTSNE is a modular Python implementation of t-Distributed Stochasitc Neighbor Embedding (t-SNE) [1], a popular dimensionality-reduction algorithm for visualizing high-dimensional data sets. openTSNE incorporates the latest improvements to the t-SNE algorithm, including the ability to add new data points to existing embeddings [2], massive speed improvements [3] [4], enabling t-SNE to scale to millions of data points and various tricks to improve global alignment of the resulting visualizations [5].

Macosko 2015 mouse retina t-SNE embedding

A visualization of 44,808 single cell transcriptomes obtained from the mouse retina [6] embedded using the multiscale kernel trick to better preserve the global aligment of the clusters.