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| TROM-package | Transcriptome Overlap Measure |
| bs.trom | Between-species transcriptome mapping |
| choose.z | Choose the suggested threshold of Z-scores |
| find.top.GO.slim.terms | Find top enriched GO slim terms |
| find.top.GO.terms | Find top enriched GO terms |
| GO_slim_id | GO slim IDs |
| heatmap.3 | Plot TROM scores in a heatmap. |
| select.associated.genes | Select the associated genes for biological samples of a species |
| select.associated.orthologs | Select the associated genes for biological samples of a species among the genes with orthologs in the other species |
| TROM | Transcriptome Overlap Measure |
| ws.trom | Within-species transcriptome mapping |
| ws.trom.orthologs | Within-species transcriptome mapping using ortholog genes |