aertslab/CREsted: 1.1.0
Year: 2024
Type: software
Abstract: 1.1.0 Features enhancer design plotting and calculation functions in the crested.tl.Crested object new module crested.tl.modisco with enhancer code analysis functionality new plots for enhancer code analysis in crested.pl.patterns new plot for sequence prediction in crested.pl.bar hidden utility functions now public in crested.utils (such as one hot encoding) CosineMSELog loss now default in peak_regression configs instead of CosineMSE tangermeme tomtom option in tfmodisco functions get_embeddings based on layer name in crested.tl.Crested crested.utils.EnhancerOptimizer utility function crested.utils.permute_model utility, useful for using with other toch packages crested.utils.extract_bigwig_values_per_bp utility improved correlation calculation speed in heatmaps Tutorials introductory notebook is updated with new functionality new enhancer code analysis tutorial Bug Fixes transfer Learning function now doesn't expect the dense block anymore bigwigs importing checks if it can open the file instead of looking for .bw extension no more ambiguous names in bed importing version requirement for modiscolite general pattern matching code bugfixes Breaking Changes utility functions and logging moved to crested.utils tfmodisco functionality moved to crested.tl.modisco Other general documentation fixes style checks now enforced on push both tf and torch backend tests on push
Institutions: KU Leuven, VIB.AI
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204274268