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savvas-paragkamian / crete_soil_microbiome

This repository contains scripts for the analysis of the Island Sampling Day of Crete 2016, a project of the soil microbiome.
GNU General Public License v3.0
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U-CIE for colouring samples of ISD #3

Closed savvas-paragkamian closed 1 year ago

savvas-paragkamian commented 1 year ago

Use the U-CIE tool to assign a colour to each sample.

Which dimensionality reduction algorithm to use?

Read Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data.

savvas-paragkamian commented 1 year ago

See Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data for the UMAP dimension reduction method prior to U-CIE

savvas-paragkamian commented 1 year ago

This is now implemented, see this commit and this.