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blessy is a module within the longhaul package for performing differential analysis on a novel genomic feature termed 'Domain Combination' or 'DoCo' for short.

In the figure below, the hypothetical gene A has 4 transcripts (Tx1, Tx2, Tx3, Tx4). On each transcript, regions that encode for protein domains (PD1, PD2) can be found. Transcripts with the similar domain phasing are categorized into the same 'Domain Combination' or 'DoCo' group. DoCo class is then considered per gene, making DoCo an intermediate feature of gene and transcript. Of note, transcripts with no domain (Tx4) are still categorized into an ‘empty’ DoCo group (;;; geneA).

The DoCo class can be used to check and group transcripts of an existing RNA-Seq count. Besides making transcript groups with equivalent biology, the count of each DoCo is the aggregated count of its component transcripts, addressing the previous issue of low count per feature in differential transcript analyses such as DTE or DTU.