merge for v1.4 #62
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merge for v1.4 #62
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- also add glycoproteomics_data_loader
…tches for named motifs
(GlcNAc & 6S would be two separate transfers)
- get_possible_topologies now can filter by physiological extensions - added extend_glycans and extend_network to, in principle, extend biosynthetic networks based on observed reactions and physiological extensions
- also filter out PTMs in extend_networks (for now)
alr_transform fixes
- mz_to_composition as a default now looks for all glycan classes & adducts + doubly-charged can be switched off now - extend_network allows users now to restrict permitted sequence contexts for extension to only contexts found in the input network
- also kick out adducts from default mz_to_composition extras
…ate_graph_features
- add adduct functionality to mz_to_composition - fine-tune ? handling in choose_correct_isoform - fix glycoproteomics formatting in process_for_glycoshift
- more options in get_heatmap GUI - explicit show_all keyword argument in get_heatmap - support already one-hot encoded labels in Poly1CrossEntropyLoss
- updated datasets and lib - version bump - update SweetNet and representations - better model versioning
- updated LectinOracle - new glycoproteomics dataset - error messages for GUI - recalculated glycan_type in sugarbase
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