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* Fixed DEG layer retrieval * Use-case tutorial icons * Restructure tutorial page * Subgroup tutorials
* Add uncertainty score in KNN label_transfer in PerturbationSpace Certainty is quantified as the fraction of nearest neighbors belonging to the classified (i.e. the most abundant) label compared to the total number of nearest neighbors. * Update pre-commit-config.yaml Replaces yanked dependency of mypy "types-pkg-resources" with "types-setuptools" as recommended: https://pypi.org/project/types-pkg-resources/ * Improve label imputation in PerturbationSpace class Key changes: - Now uses KNN graph in adata: saves cost and increases consistency - Vectorized operations instead of expensive for loop - Distance weighting for KNN imputation - Quantifies uncertainty as local KNN label entropy
* Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
* Augur scsim warnings Signed-off-by: zethson <[email protected]> * Submodules Signed-off-by: zethson <[email protected]> * Add super draft of pertpy validator Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Polish Signed-off-by: zethson <[email protected]> * Nested try Signed-off-by: zethson <[email protected]> * validator in test Signed-off-by: zethson <[email protected]> * try uv for rtd Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv Signed-off-by: zethson <[email protected]> * rtd uv fix Signed-off-by: zethson <[email protected]> * mb sphinx fix for validator Signed-off-by: zethson <[email protected]> * docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> * remove PerturbationValidator from docs Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
* Fix jax random array Signed-off-by: zethson <[email protected]> * Fix further jax warnings Signed-off-by: zethson <[email protected]> * Fix edger Signed-off-by: zethson <[email protected]> * Fix choice Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]>
* Switch to formulaic-contrasts * Cleanup * removing design matrix workaround (#691) Co-authored-by: Emma Dann <[email protected]> * Fix PyDESeq2 * Update tests * fix typo in gitignore * Remove contrast dataclass, which isnt used anywhere * Fix edgeR rpy2 tests (#692) * fix broken rpy2 edger tests * updated edger tests * Fix tests (scipy) Signed-off-by: zethson <[email protected]> * submodule Signed-off-by: zethson <[email protected]> * Remove unused code Signed-off-by: zethson <[email protected]> * type hints Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: Emma Dann <[email protected]> Co-authored-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Signed-off-by: zethson <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Signed-off-by: Lukas Heumos <[email protected]>
* Fix probability data type Signed-off-by: Lukas Heumos <[email protected]> * Optimize mean_var distance Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]>
* Try buildjet Signed-off-by: Lukas Heumos <[email protected]> * Try buildjet large Signed-off-by: Lukas Heumos <[email protected]> * speed up predict_differential_prioritization Signed-off-by: Lukas Heumos <[email protected]> * speed up tests Signed-off-by: Lukas Heumos <[email protected]> --------- Signed-off-by: Lukas Heumos <[email protected]>
Signed-off-by: Lukas Heumos <[email protected]>
Signed-off-by: Lukas Heumos <[email protected]>
* Removed show parameter * Adapt plotting API for Augur, Coda, Dialogue * Adapted plotting API for Milo, Mixscape, scgen * Add joblib * Remove joblib --------- Co-authored-by: Lukas Heumos <[email protected]>
Signed-off-by: Lukas Heumos <[email protected]>
…695) * Added Mixscape seeds and test * Added manual reference cell selection method * Updated docs method descriptions * Merged main into branch * Fixed merge conflict * Merged main * Added citation to docs * Renamed 'manual' selection mode to 'split_by'
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