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Scanpy DiffusionMap (version 1.8.1+3+galaxy0)

Calculate Diffusion Components (

Calculate diffusion components from single cell KNN graphs.

This requires to run Scanpy ComputeGraph, first.

It yields X_diffmap, the dimension-reduced representation in diffusion components space.

More information can be found at

Version history

1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.

1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.

1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.

1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.

1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.

1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team at EMBL-EBI

1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.

1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.

1.4.3+galaxy10: Use profile 18.01 for modules.

1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.

1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).

1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).

1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team at EMBL-EBI and Teichmann Lab at Wellcome Sanger Institute.