Supply more output files in tutorial about schicexplorer

[zhqu1148980644]

@joachimwolff Would you please share with us the output .txt file of each clustering method?

[joachimwolff]

Thank you for the reminder, I will take care of it.

[joachimwolff]

These are the requested files, computed on Nagano 2017 data with 1275 cells for which the cell labels were provided by Nagano. This is a different interaction matrix as mentioned in the tutorial: https://zenodo.org/record/4308298/files/nagano_1mb_cell_type.scool

The dataset and the cell labels are part of a publication that is currently under review: https://zenodo.org/record/4308298#.X_XnWFNKiic

To compute the PCA, a small bug fix was required, see code in the develop branch. All used commands to compute the results have been computed with scHiCExplorer version 7 from the develop branch, please see commands.txt for the individual commands.

Small side note: only the MinHash based computation creates reasonable clustering results. This can be seen by correlating the clusters with the labeled data provided by Nagano.

I hope this suits your expectations and please let me know if I can help you otherwise.

Best,

Joachim

minhash.txt
pca_cluster.txt
raw_cluster.txt
scikit_knn_cluster.txt
svl_results.txt
compartments_clustering.txt

commands.txt

[zhqu1148980644]

Thank you for your sharing.