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swan v2.5
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@fairliereese fairliereese released this 25 Jan 23:45
· 35 commits to master since this release
v2.5
0acbb9c

Swan 2.5

SwanGraph structure changes

  • Counts and other expression structure (ie TPM, PI) are now stored as sparse matrices to massively save on on-disk as well as in-memory storage
  • Capability of storing gene-level abundance information (SwanGraph.gene_adata) calculated separately from transcript-level
  • Added AnnData to store intron chain level abundance information (SwanGraph.ic_adata)
  • Added tracking for stable gene ID in cases where reference annotation versions don't match (ie ENSG000000014.5 --> ENSG000000014)

Native compatibility with cerberus transcriptomes

  • Will track TSSs, ICs, and TESs called by cerberus based on the names of transcripts provided from the GTF

Other changes

  • DIE test now reports top 2 DPI isoforms
  • Faster counts and TPM calculations using Scanpy tools
  • Added option to sort by isoform's cumulative PI value in the gene report sorting
  • Added plotting option for plotting browser models directly on to a preexisting Matplotlib axis SwanGraph.plot_browser()
  • Added plotting option to plot bed regions SwanGraph.pg.plot_regions()
  • Added options to calculate TPM across multiple datasets as either the minimum or maximum of the values between the datasets

Minor bug fixes

  • Fixed DIE test bug when there are >11 isoforms / gene
  • Fixed bugs in SwanGraph.gen_report()
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