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https://github.com/fomightez/cluster_analysis-binder

Demonstrating various clustering algorithms in Python, all provided actively useable via MyBinder.org.
https://github.com/fomightez/cluster_analysis-binder

Last synced: 21 days ago
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Demonstrating various clustering algorithms in Python, all provided actively useable via MyBinder.org.

Host: GitHub
URL: https://github.com/fomightez/cluster_analysis-binder
Owner: fomightez
License: mit
Created: 2020-07-01T17:50:19.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2024-12-11T16:32:35.000Z (about 1 month ago)
Last Synced: 2024-12-11T17:34:43.630Z (about 1 month ago)
Language: Jupyter Notebook
Size: 4.58 MB
Stars: 0
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/cluster_analysis-binder/master?filepath=index.ipynb)

# cluster_analysis-binder
Demonstrating various clustering algorithms and associated visualizations in Python, all provided in and actively useable form via MyBinder.org.

Click any 'launch binder' badge on this page to get started.

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### Details

See [Avoiding common pitfalls when clustering biological data](https://stke.sciencemag.org/content/9/432/re6) by Tom Ronan, Zhijie Qi, and Kristen M. Naegle (2016) for useful background.

Notebook content demonstrates:

- Hierarchical clustering
- Block model and Bi-clustering
- k-means clustering
- DBSCAN clustering (DBSCAN = Density-Based Spatial Clustering of Applications with Noise)
- HDBSCAN clustering (HSBSCAN = Hierarchical Density-Based Spatial Clustering of Applications with Noise)
- Comparing clustering results
- Examining variation in clustering results

Links to [a demo](https://github.com/cornhundred/citibike-clustergrammer2) that uses [clustergrammer2](https://clustergrammer.readthedocs.io/clustergrammer2.html), which is an interactive heatmap Jupyter widget built to help researchers interactively explore single cell data (e.g. scRNA-seq). Although that is not the type of data used in the demonstration.

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#### Technical notes

This repository builds largely on [my binderized 3D scatter plot repostiory](https://github.com/fomightez/3Dscatter_plot-binder) for the needed packages as I started development there. I later added Scikit-Learn (Sklearn) so didn't need to install it in this repostiory. Kept advanced items from [my binderized 3D scatter plot repostiory](https://github.com/fomightez/3Dscatter_plot-binder) even though not intially needed here because I hope to add the use of widgets for adding data here as well.

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[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/fomightez/cluster_analysis-binder/master?filepath=index.ipynb)