LIANA+: an all-in-one framework for cell-cell communication
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.
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: https://github.com/saezlab/liana-py/compare/1.0.4...1.0.5
See Release notes
See release notes.
See Release Notes
See Release notes
This of LIANA+ was used to generate all of the results presented in the preprint.
See https://liana-py.readthedocs.io/en/latest/release_notes.html for details
Stable Release v0.1.8