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Automatic determination of optimal cluster number

JK Jakob Nikolas Kather

Last updated date: Feb 20, 2020 Views: 1208 Forks: 0

original An abbreviated version of this protocol was published in eLife in Sep, 2018
Topography of cancer-associated immune cells in human solid tumors
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Thank you very much for your interest in our work! The Matlab script that was used to determine the optimal number of clusters can be found here: https://github.com/elifesciences-publications/immuneTopography/blob/master/step_03b_findOptimClust.m The core function in this script is the Matlab function "evalclusters" which is extensively documented here: https://de.mathworks.com/help/stats/evalclusters.html. These links should allow you to reproduce the procedure for your project. Hope that helps!

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Kather, J(2020). Automatic determination of optimal cluster number. Bio-protocol Preprint. bio-protocol.org/prep219.
  2. Kather, J. N., Suarez-Carmona, M., Charoentong, P., Weis, C., Hirsch, D., Bankhead, P., Horning, M., Ferber, D., Kel, I., Herpel, E., Schott, S., Zörnig, I., Utikal, J., Marx, A., Gaiser, T., Brenner, H., Chang-Claude, J., Hoffmeister, M., Jäger, D. and Halama, N.(2018). Topography of cancer-associated immune cells in human solid tumors. eLife. DOI: 10.7554/eLife.36967

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