1.8.0

Features

• Human brain models from the ASAP preprint are now available in the model repository! (#200)
• crested.pl.explain.contribution_scores, crested.pl.locus.track, and crested.pl.design.step_contribution_scores now take the x_shift parameter, which lets you shift the zoom window around. (#140, #202)
• crested.pp.change_regions_width now stores the unresized index in adata.var and allows manually passing crested.Genome objects (#201)
• crested.pl.modisco.clustermap_tf_motif colorbar and label padding improved (#140).
• tl.modisco function defaults updated: match_to_patterns sim_threshold 0.5 -> 7.0, crested.tl.modisco.process_patterns sim_threshold 3.0 -> 6.0, trim_ic_threshold 0.05 -> 0.025 (#140)
• Reworked crested.tl.modisco's match_to_patterns to be vectorized (#140)
• Reworked crested.tl.modisco's post_hoc_merging function. The old function is preserved as post_hoc_merging_old. The new function can return merge metadata with new parameter return_info (#140)

Bugfixes

• Memory usage of crested.tl.predict reduced significantly and fragmentation prevented (#199)
• crested.pp.change_regions_width now preserves strand information (#201)
• crested.pp.change_regions_width now uses the region names as starting point, rather than adata.var['start'/'end'], to make behaviour consistent across the package (#201)
• crested.pl.corr.heatmap/crested.pl.corr.heatmap_self now properly set the default layout engine, stopping warnings when using pre-existing axes (#198)
• Removed deprecated internal Crested object methods. Their associated public methods were removed in v1.7.1, after already being deprecated in v1.3 (#198)
• Duplicate kwargs in main body and imshow_kws of crested.pl.modisco.clustermap_tf_motif fixed (#140)

Documentation

• Updated links/citations from CREsted preprint to CREsted paper 🎉 (#198)
• Updated model citations in general for consistency (#198)
• Enhancer code analysis notebook updated (new pattern clustering and more) (#140)