| breaks | breaks |
| c | c |
| cgChain | cgChain |
| cn | cn |
| dim | dim dimension of chain is @n x @m |
| expand | expand |
| gChain | gChain |
| gChain-class | gChain-class |
| genomes | genomes |
| gMultiply | gMultiply |
| grl.split | grl.split |
| gr.refactor | gr.refactor |
| gr.tostring | gr.tostring |
| gSubset | gSubset |
| gUnique | gUnique |
| initialize | initialize |
| lift | lift |
| links | links returns links associated with chain |
| maChain | maChain |
| paChain | paChain |
| pads | pads |
| scale | scale |
| seqinfo | seqinfo |
| spChain-open-paren-spliced-chain-close-paren | spChain |
| squeeze | squeeze |
| sub | [ |
| t | t |
| txChain | txChain |
| values | values |
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