Methods and apparatus provide PCI Express support on a programmable device. A device includes a hard-coded transceiver that supports functionality associated with the PCI Express physical layer and link layer. The hard-coded transceiver can also support part of the PCI Express transaction layer. Soft-coded logic is used to support higher layer functionality including a portion of the transaction layer to allow custom configuration of PCI Express features such as virtual channels, buffers, prioritization, and quality of service characteristics. The hybrid solution reduces logic resource cost and provides an effective custom configurable solution.