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CellBender 0.3.0 release
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@sjfleming sjfleming released this 08 Aug 18:51
· 10 commits to master since this release
v0.3.0
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Learn about vigilant mode.

This release coincides with the publication of our manuscript in Nature Methods. https://doi.org/10.1038/s41592-023-01943-7

Changes from previous versions include:

  • Output report in HTML format
  • Code produces checkpoints, useful for automatic restarting of WDL workflow without losing progress (enabling use of preemptible GPUs on Terra, and potentially better use of Google Colab GPUs for free)
  • Model includes new safeguards on count removal per gene, and treats the construction of the output count matrix as an auxiliary optimization problem
  • --expected-cells and --total-droplets-included input arguments are not typically needed, as default behavior is very much improved
  • The full posterior gets saved as an output h5 file
  • Smoother learning curves and improved performance on tricky samples
  • Bug fixes
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