Swan 3.0

SwanGraph initialization

• Added bool options to SwanGraph initialization (edge_adata, end_adata, and ic_adata) that the user can set to False if they don't wish to track abundance for these individual transcript features

AnnData compatibility

• Allows for addition of abundance information directly from an AnnData object; bypassing dense-matrix representations of the data (SwanGraph.add_adata())

Documentation

• Updated sample data links
• Added AnnData data format to the file format specs
• Added additional examples to showcase functionality added in v3.0 and 2.5

Deprecation of differential gene and transcript expression tests

• Deprecated SwanGraph.de_gene_test() and SwanGraph.de_transcript_test() as I have not had luck running diffxpy in a while
• Added example tutorial on how to directly use a Swan AnnData to perform differential expression testing with PyDESeq2

Known issues

• Currently Cerberus does not output transcript novelty assignments to GTFs and they are therefore not parsed by Swan; will fix in a future update