https://github.com/rikenbit/onlinePCA-experiments

https://github.com/rikenbit/onlinePCA-experiments

Last synced: 27 days ago
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• Host: GitHub
• URL: https://github.com/rikenbit/onlinePCA-experiments
• Owner: rikenbit
• License: other
• Created: 2019-05-16T00:28:30.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2019-10-02T07:14:15.000Z (about 5 years ago)
• Last Synced: 2024-02-15T10:37:16.323Z (10 months ago)
• Language: Shell
• Size: 66.4 KB
• Stars: 4
• Watchers: 13
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# onlinePCA-experiments

[![DOI](https://zenodo.org/badge/186921547.svg)](https://zenodo.org/badge/latestdoi/186921547)

## About data preparation

- **PBMCs** : Data/PBMCs/README

- **Pancreas** : Data/Pancreas/README

- **BrainSpinalCord** : Data/BrainSpinalCord/README

- **Brain** : Data/Brain/README

## Requirements

- **GNU Time** : v1.7

- **Open Grid Scheduler/Grid Engine** : v2011.11

- **R** : v3.5.0

- **Python** : v3.6.4

- **Julia** : v1.0.1

- **Rake (Ruby)** : v11.2.2

## How to perform all the PCA scripts

```{bash}

cd Analysis

rake install # Package installation

rake preprocess # Preprocessing the data files

rake benchmark # Benchmarking all the PCA implementations

```

## Result of the banchmarking

- **Eigenvectors** : Data/{PBMCs,Pancreas,BrainSpinalCord,Brain}/*[Each PCA]*/Eigen_vectors.csv

- **Eigenvalues** : Data/{PBMCs,Pancreas,BrainSpinalCord,Brain}/*[Each PCA]*/Eigen_values.csv

- **Elapsed time and memory usage** : Analysis/log/*