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The mod is fully compatible with the Forge Energy (FE) system. The Transmutation Generator can power machines from mods like Thermal Expansion, Mekanism, and Actually Additions.

Inventory Tweaks: Machine GUIs are compatible with sorting shortcuts.
Applied Energistics 2 / Refined Storage: You can place a Transmutation Chamber against an Interface. By setting the Chamber to produce a specific item, the storage system will see the Chamber's output buffer as available inventory.
Pipes: All machines support standard side-based insertion and extraction.
Chamber: Extract from sides/bottom.
Disassembler: Insert from any side.
Generator: Energy can be extracted from any side.