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@zktuong zktuong released this 30 Mar 18:20
· 1259 commits to master since this release
v0.1.0
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Bug fixes and updates:

  • Github actions - tests
    Fixed issue with tests failing. Mostly resolved.

  • find_clones and generate_network
    Bugs were introduced with the v0.028 due to the rework of dandelion initialization causing some clones to be excessively splitted (multiple '|' separators), IgM/IgD catcher was skipping a few steps unnecessarily, and networks were not generating properly due to incorrect index referencing. This has now been corrected. Switched back to using squareform + pdist for calculating distances to simplify the code. May revisit in the future.

  • filter_bcr
    Similar issue as above, contigs with multiple IgH were not flagged properly and this resulted in extremely noisy data. This is now fixed and the IgM|IgD catcher is actually working properly now! Also added a productive_only toggle to only retain bcrs that are determined to be productive. Allow the user the flexibility to change this. Perhaps i should add the same toggle to all other functions so that the contigs can pass through and be flexibly used in subsequent steps?

  • update_metadata
    Found some typos.

  • quantify_mutation
    Fixed issue where original code wasn't allowing for the R-objects to be parsed properly when specifting non-NULL arguments.

  • miscellaneous
    updated codes to prevent syntax warnings.

  • annotation
    All main functions visible to user are annotated. Can be improved further for clarity but for next version update.

Still needs work

  • plotting issues
    There's an issue in reassign_alleles where sometimes plotting fail. I've added a try-except step to try and circumvene the error while i search for what it actually is.

  • metadata info
    I think a column is needed to deal with multi-chain flagging properly. It's currently not ideal as IgM/IgD cells can be flagged as multi and calling them single isn't the right solution.

New features:

  • Integration with scirpy
    Dandelion can read scirpy's processed output. Related to scverse/scirpy#240
    Will update when scirpy's AirrCell class is fully implemented.

Depreciated:

Assets 2