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Releases: saezlab/liana-py

1.4.0

02 Sep 10:20
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1.3.0

18 Jul 11:49
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1.2.1

12 Jun 07:42
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  • v1.2.1 by @dbdimitrov in #119
  • set required Python to >=3.8: the <3.12 causes a broad incompatibility issue in package management by @deeenes in #114

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Full Changelog: 1.2.0...1.2.1

1.2.0

24 May 18:30
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1.1.0

12 Apr 09:01
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1.1.0 (12.04.2024)


  • Added a check for the subset of cell types in li.multi.dea_to_lr. Related to #92.

  • Split Local and Global Bivariate metrics. Specifically, I reworked completely the underlying code, though the API should remain relatively unchanged. With the exceptions of: 1) lr_bivar is now removed and bivar has been renamed to bivariate. This allowed me to remove a lot of redundancies between the two functions. 2) nz_threshold has been renamed to nz_prop for consistency with expr_prop in the remainder of the package. Related to #44.

  • li.mt.bivariate parameter mod_added has been renamed to key_added due to this now refer to both .obsm and .mod - depedening whether an AnnData or MuData object is passed.

  • Added Global Lee's statistic, along with a note on the weighted product that upon z-scaling it is equivalent to Lee's local statistic.

  • The Global L statistic and Global Moran's R are themselves basically identical. See Eq.22 from Lee and Eq.1 in Supps of SpatialDM.

  • Changed the li.mt.bivar parameter function_name to local_name for consistency and to avoid ambiguity with the newly-added global_name parameter.

  • Added bumpversion to manage versioning. Related to #73.

  • Added max_runs and stable_runs parameters to enable the inference of robust causal networks with CORNETO. Related to #82.

  • Optimized MISTy such that the matrix multiplication by weights is done only once, rather than for each target. Users can now obtain the weighted matrix via the misty.get_weighted_matrix function.

  • MISTy models are now passed externally, rather than being hardcoded. This allows for more flexibility in the models used. As an example, I also added a RobustLinearModel from statsmodels. Related to #74.

  • Removed forced conversion to sparse csr_matrix matrices in MISTy. Related to #57.

1.0.5

14 Mar 06:34
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  • Added ScSeqComm Method, implemented by @BaldanMatt (#68)

  • Added functions to query a metabolite-receptor interactions database (MetalinksDB), including:
    => li.rs.get_metalinks to get the database
    => li.rs.get_metalinks_values to get the distinct annotation values of the database
    => describe_metalinks to get a description of the database

  • Added a metabolite-mediated CCC tutorial in spatially-resolved multi-omics data (#45).

  • Changed hardcoded constants to be defined in _constants.py

  • Excluded CellChat from the default rank_aggregate method

  • Fixed return logic of SpatialBivariate

  • li.mt.process_scores is now exported to li.mt

  • Changed the default max_neighbours in li.ut.spatial_neighbors to 1/10 of the number of spots.

Full Changelog: 1.0.4...1.0.5

1.0.4

17 Jan 16:09
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v1.0.3

10 Nov 18:52
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v1.0.2

26 Oct 06:45
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1.0.1 Stable Release

01 Oct 21:49
ef2df80
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