| assessGrouping | assessGrouping | 
| bindingContextDistance | bindingContextDistance | 
| bindingContextDistanceCapR | bindingContextDistanceCapR | 
| CleanBAMtoBG | CleanBAMtoBG | 
| CleanBEDtoBG | CleanBEDtoBG | 
| ExtractTranscriptomeSequence | ExtractTranscriptomeSequence | 
| GenomeMappingToChainFile | GenomeMappingToChainFile | 
| getChainChrSize | getChainChrSize | 
| get_outfiles | get_outfiles | 
| liftOverToExomicBG | liftOverToExomicBG | 
| nearBynding-package | Discern RNA structure proximal to protein binding | 
| processCapRout | processCapRout | 
| runCapR | runCapR | 
| runStereogene | runStereogene | 
| runStereogeneOnCapR | runStereogeneOnCapR | 
| visualizeCapRStereogene | visualizeCapRStereogene | 
| visualizeStereogene | visualizeStereogene | 
| write_config | write_config | 
| write_fasta | write_fasta | 
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