Changelog

v1.0

Main components of scallop:

  • sl.Scallop and sl.Bootstrap objects.

  • tl: sl.tl.getScore() .

  • pl: sl.pl.plotScore().

  • datasets: sl.datasets.delete_datasets() and sl.datasets.joost2016().

v1.0.1

Fixed pip dependencies.

v1.0.2

Corrected calculation of freqScore to range between 0 and 1.

v1.0.3

Fixed minor issues.

v1.0.4

Corrected scallop clustering use_weights parameter inferred from scanpy’s.

v1.1.0

  • Added logging support.

  • Implemented parallelization of sl.tl.getScore().

  • Added louvain to clustering algorithms.

  • Added 10x mouse brain and heart 10k datasets.

  • Remapping of unknown clusters.

v1.1.1

Corrected error on sampling for bootstrap part of sl.tl.getScore(). When bootstrapping, a set of random indices are selected. If frac_cells=1 then all indices are selected. However, those indices were randomized, and even with the same seed value, clustering would yield different results. Fixing the issue implies to sort the selected indices, regardless of frac_cells selected.

v1.2.0

  • Implemented force option for sl.tl.getScore().

  • Applied some assertions on sl.tl.getScore().

  • Added dictionary of arguments to add seed to parallel calculation of bt_matrix.

  • Added seed_in_bt as argument for sl.tl.getScore().

  • Corrected seed_in_bt to solve None problem from leiden. In some datasets, if seed is None, the random generation algorithm only considers 6-or-so different seeds.

v1.3.0

  • Ensure compatibility with latest Scanpy AnnData structure (v1.8).

  • Complete the documentation.

  • Ensure compatibility with ray latest version.

  • Minor fix in nan management during freqScore calculation.