Cytobank: providing an analytics platform for community cytometry data analysis and collaboration.

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HemI: A Toolkit for Illustrating Heatmaps (2014, background): “Moreover, although heatmaps can be accomplished by a number of commercial or non-commercial softwares such as GeneSpring GX, Mayday [6], Cytobank [7] and D3 (http://d3js.”
Automated Optimal Parameters for T-Distributed Stochastic Neighbor Embedding Improve Visualization and Allow Analysis of Large Datasets (2018, methodology): “While opt-SNE and t-SNE both capture the macro-structure illustrated by gene overlays, several Louvain clusters (3, 18, 19, 25, 28) appear partially or completely overlapped by other clusters in standard t-SNE but not in the opt-SNE embedding.”