Releases: saezlab/liana-py
1.1.0
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 andbivar
has been renamed tobivariate
. This allowed me to remove a lot of redundancies between the two functions. 2)nz_threshold
has been renamed tonz_prop
for consistency withexpr_prop
in the remainder of the package. Related to #44. -
li.mt.bivariate
parametermod_added
has been renamed tokey_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
parameterfunction_name
tolocal_name
for consistency and to avoid ambiguity with the newly-addedglobal_name
parameter. -
Added
bumpversion
to manage versioning. Related to #73. -
Added
max_runs
andstable_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
What's Changed
- v1.0.5 by @dbdimitrov in #91
-
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 toli.mt
-
Changed the default
max_neighbours
inli.ut.spatial_neighbors
to 1/10 of the number of spots.
Full Changelog: 1.0.4...1.0.5
1.0.4
See Release notes
v1.0.3
See release notes.
v1.0.2
See Release Notes
1.0.1 Stable Release
See Release notes
Biorxiv Release
This of LIANA+ was used to generate all of the results presented in the preprint.
LIANA+ first alpha release
Merge pull request #39 from saezlab/dev LIANA+ merge
0.1.9
See https://liana-py.readthedocs.io/en/latest/release_notes.html for details
0.1.8
Stable Release v0.1.8