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Splenocyte

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Qiao Liu edited this page Aug 28, 2020 · 7 revisions

Tutorial on Splenocyte dataset

Installation

git clone https://github.com/kimmo1019/scDEC.git

Downloaded Splenocyte dataset which has been formatted as input of scDEC from the zenode repository. Note that it should be located in the datasets folder.

Run scDEC

python main_clustering.py --data Splenocyte --K 12 --dx 10 --dy 20

The training will take about 20 mins on a Linux server with Xeon(R) E5-2680 CPUs and a Tesla P100 GPU. The results will be saved in the results/Splenocyte/20200820_163135_x_dim=10_y_dim=20_alpha=10.0_beta=10.0_ratio=0.2 folder.

python eval.py --data Splenocyte --timestamp 20200820_163135

Visualization

The visualization of latent features will be saved as scDEC_embedding.png in the same result folder.

Clustering results

The clustering results will be saved as scDEC_cluster.txt. Each row denotes the predicted cluster id of each cell.

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