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Oct 23, 2020
Bioinformatics
Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.
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Setup
Seen with latest code from git while preparing the 1.73 release on Linux, but applies to all platforms.
Expected behaviour
$ python run_tests.py test_PDB_StructureAlignment.py
Python version: 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Operating system: posix linux2
test_PDB_StructureAlignment ... ok
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This bug only occurred in 1.6.0 but not 1.5.0
I was running scanpy 1.6.0 this:
sc.tl.filter_rank_genes_groups(adata, groupby=obs,\ max_out_group_fraction=max_out_group_fraction, min_fold_change=min_fold_change,use_raw=use_raw, min_in_group_fraction=0.25,log=log)
But got this error:
Filtering genes using: min_in_gro
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