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Sparse Scanpy Speedups

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@adamgayoso adamgayoso released this 12 Jul 16:55
v2.5
95b2db1
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Learn about vigilant mode.
  • Improves installation process through one pip install command and removes requirements.txt
  • Adds documentation
  • Uses sparse matrices for raw counts in the backend for speedups
  • Uses scanpy for log normalization and PCA and optionally clustering
  • New use_phenograph option to disable PhenoGraph and use Louvain as implemented in scanpy (much faster)
  • Adds binary verbose option. Set to True to turn on informational messages (previous default behavior).
  • Replaces tsne plot with umap and no longer clusters data, just visualizes doublets on the umap
  • With new scanpy integration, doubletdetection requires at least Python 3.6.
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