| dot-combineMatchingTranscripts | Combining matching transcripts |
| dot-scoreByTranscripts | Ranking matching transcripts |
| dot-txs2genesym | Adding gene symbol annotations |
| grapes-na-grapes | Replaces the NA values in a with corresponding values in b |
| grapes-null-grapes | Uses b if a is NULL |
| rtDetect | Detecting retrotranscript insertion in nuclear genomes. |
| svaRetro | svaRetro: a package for retrotransposed transcript detection |
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