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  "Title": "Retrotransposed transcript detection from structural variants",
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  "Description": "svaRetro contains functions for detecting retrotransposed\ntranscripts (RTs) from structural variant calls. It takes\nstructural variant calls in GRanges of breakend notation and\nidentifies RTs by exon-exon junctions and insertion sites. The\ncandidate RTs are reported by events and annotated with\ninformation of the inserted transcripts.",
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