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@LukasMahieu LukasMahieu released this 16 Jan 14:13
· 1 commit to main since this release
1.2.0
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Learn about vigilant mode.

1.2.0

This version accompanies the human neural development paper preprint.

Features

  • updated to scverse template v0.6.0
  • added parameter to select pca svd solver for running PCA instead of hardcoded "covariance_eigh"
  • added functionality to save and load patterns to and from disk (tfmindi.save_patterns and tfmindi.load_patterns)
  • now allows for patterns to be generated by any annotation in .obs, not only by leiden
  • can now concatenate multiple TF-MINDI anndatas together using tfmindi.concat
  • changed behaviour of seqlet most frequent-occurence for annotating clusters to binomial tests
  • added MAFFT-based backend as option for pattern creation (much faster than TomTom or k-mer)

Bugfixes

  • fix extra 0-position being included in Pattern.ic_trim
  • fix failure case in in Pattern.ic_trim when all nucleotides are above IC threshold
  • plotting legends are filtered on colors in adata.obs[color_by]
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