Test reproducibility of leiden/umap on different systems

Related tags

Miscellaneousscanpy_reproducibility
Overview

Test reproducibility of leiden/umap on different systems

This nextflow pipeline runs a jupyter notebook that runs

sc.pp.neighbors
sc.tl.umap
sc.tl.leiden

on a test dataset with a pre-computed latent representation stored in adata.obsm["X_scVI"].

The test-dataset is available in the data directory.

Running the pipeline

There are a few minor things you may need to adjust on your system:

  • The run_pipeline.sh script starts nextflow with a work directory and a profile specific to our institute.
  • The clusterOptions is used to submit the jobs to different nodes on our HPC and is specific to our queue and node names.
  • The node names are passed on to clusterOptions from a channel defined in main.nf.

Results

The results (tested on 5 nodes, 4 of which have different CPUs) are available from: https://grst.github.io/scanpy_reproducibility/

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Comments
  • Inquiry: any explanations?

    Inquiry: any explanations?

    Hello,

    I observed exactly the same thing as you showed in the demonstration, when it differs, the global structure in 2D UMAP seems similar but there will be displacements in each specific region.

    I was wondering, would you happen to have some explanations for that? Since the randomness should have been controlled by specifying the seed.

    Thanks, Frank

    opened by frankligy 1
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Gregor Sturm
Always stay curious!
Gregor Sturm
GitHub Repository https://grst.github.io/scanpy_reproducibility/
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