Upgrade Mana Potion - Upgrades 10x Mana potions to 5x of the next tier.

Upgrade Health Potion - Upgrades 10x Health potions to 5x of the next tier

Unlock Enchants - Unlock all Enchants on any weapon by transmuting it with x25 Keys.

Level Up Item - Transmuting a low level item with a high level item of the same quality will boost the low level item to match the high level item's level. Destroys the high level item in the process.

Random Unique - Consumes 3x Unique items for a new, random Unique item. If all 3x items are of the same slot, such as 3 weapons, a new weapon fitting your class will be generated. If not, a randomly selected item is generated.

Random Legendary - Consumes 3x Legendary items for a new, random, Legendary item. If all 3x items are of the same slot, such as 3 weapons (of any kind), a new weapon fitting your class will be generated. If not, a fully randomly selected item is generated.

Empower Legendary - Empowers a Legendary item, increasing the base stats to match a True Legendary of choice. The Legendary and True Legendary must be the same level and item type (you can only upgrade a Legendary ring with a True Legendary Ring, ect.), and 20x Champion's Crowns are needed for the Transmutation. Consumes the True Legendary item in the process.

Set Item Conversion - Sacrifices 30x Champion's Crown and a Set item of any quality to get a different item from the same set.

Random True Legendary - Consumes 5x True Legendary items for a new, random, True Legendary item. If all 5x items are of the same slot, such as 5 weapons (of any kind), a new weapon fitting your class will be generated. If not, a fully randomly selected item is generated.

Create Spell Codex - Combining a Spell Codex (legendary item drop) with 50x of any Spell Scroll creates a Codex with unlimited uses of that spell scroll.
Does not work with Challenge Scrolls.

Permanent Sphere Socket - Consumes 30x Champion's Crown and a Prismatic Sphere to socket an item with a new permanent Prismatic Sphere socket (only one prismatic socket can be applied to an item).

Permanent Cube Socket - Consumes 30x Champion's Crown and a Prismatic Cube to socket an item with a new permanent Prismatic Cube socket (only one prismatic socket can be applied to an item).

Permanent Star Socket - Consumes 30x Champion's Crown and a Prismatic Star to socket an item with a new permanent Prismatic Star socket (only one prismatic socket can be applied to an item).

Destroy Prismatic Socket - Consumes 1x Prismatic Liquid to destroy any Prismatic Socket on an item.

Random Lesser Rune - Consumes 5x Lesser Runes items for a new, fully random, Lesser Rune. Crafted Runes cannot be used or generated.

Create Lesser Rune - Consumes 50x Champion's Crown, any Unique or Legendary item with a Power on it, and a Runestone to create a Lesser Rune with the Power the item had. The item is lost in the process

Apply Lesser Rune - Consumes 50x Champion's Crown and a Lesser Rune to apply it to a fitting item.

Create Greater Rune - Consumes 50x Champion's Crown, any True Legendary item with a Power on it, and a Runestone to create a Greater Rune with the Power the item had. The item is lost in the process.

Apply Greater Rune - Consumes 50x Champion's Crown and a Greater Rune to apply it to a fitting item.

Destroy Rune - Consumes 1x Runelord's Remose to destroy any attached Rune on an item.

Craft Mythical Sword - Upgrade any Legendary class set Sword to Mythical quality with two Rune sockets by combining it with the Ancient Hilt and Ancient Blade Crafting Materials, as well as 10x of each: Tainted Blood, Enchanted Leaf, Electrified Hair, Giant Tooth, and Evil Eye. This will remove any Runes already on the Sword. The materials can be found in Greater Boss Anomalies.

Upgrade any Legendary class set Fist to Mythical quality with two Rune sockets by combining it with the Ancient Straps and Ancient Gloves Crafting Materials, as well as 10x of each: Tainted Blood, Enchanted Leaf, Electrified Hair, Giant Tooth, and Evil Eye. This will remove any Runes already on the Fist. The materials can be found in Greater Boss Anomalies.

Upgrade any Legendary class set Bow to Mythical quality with two Rune sockets by combining it with the Ancient String and Ancient Bow Crafting Materials, as well as 10x of each: Tainted Blood, Enchanted Leaf, Electrified Hair, Giant Tooth, and Evil Eye. This will remove any Runes already on the Bow. The materials can be found in Greater Boss Anomalies.

Upgrade any Legendary class set Staff to Mythical quality with two Rune sockets by combining it with the Ancient Power Crystal and Ancient Staff Crafting Materials, as well as 10x of each: Tainted Blood, Enchanted Leaf, Electrified Hair, Giant Tooth, and Evil Eye. This will remove any Runes already on the Staff. The materials can be found in Greater Boss Anomalies.

Secret Transmutation:
Grab all of the element stones (Poisonstone, Holystone, ect.) of any level and place them all into the Transmutation box, and it creates the Elementium Stone (All attacks place an Elemental Attunement on foes, increasing the damage they take by 5% - 10% [15% augment cap], each element used places a separate Attunement, lasts 7 seconds. If the stones are of a different level, it will average out when it is created.

Thanks to MKN - Heleno for this recipe:
Grab all of the caps (Nightcap, ect.) of any level and place them all into the Transmutation box and creates the Mightcap (Allows the use of two Ultimates). If the items are of a different level, it will average out when it is created.

Combining a Mk. 3 Enhanced Injector and Mk. 3 Rapid Injector in the transmutation menu will allow you to create a Mk. 4 Elixir Injector with 3 elixir sockets. The Mk.4 Elixir Injector has reduced cooldown, 30% increased Elixir Effectiveness, and 30% increased Elixir Duration.

Combining a Mk. 3 Potion Injector and 100 Sublime Health Potions in the transmutation menu will allow you to create a Mk. 4 Health Injector with 3 potion sockets. The Mk.4 Health Injector only accepts health potions, automatically triggers while in a belt slot and falling below 30% health, and has 35% increased effectiveness of slotted potions.

Combining a Mk. 3 Potion Injector and 100 Sublime Mana Potions in the transmutation menu will allow you to create a Mk. 4 Mana Injector with 3 potion sockets. The Mk.4 Mana Injector only accepts mana potions, automatically triggers while in a belt slot and falling below 30% mana, and has 35% increased effectiveness of slotted potions.

Combining a Mk. 4 Health and Mana Injector in the transmutation menu will allow you to create a Mk. 5 Super Injector with 4 potion sockets. The Mk.5 Super Injector only accepts potions, has reduced cooldown, automatically triggers while in a belt slot and falling below 30% health or mana, and has 45% increased effectiveness of slotted potions.

Combining a Catapult / Scatter launcher with a Rapid Launcher in the transmutation menu will allow you to create a Mk. 4 Rapid Catapult / Scatter launcher respectively. The Mk.4 Rapid Catapult / Scatter launchers keep their vial launching properties, but have a reduced cooldown on their use. The Mk. 4 launchers have 3 vial sockets.

Combining a Catapult and Scatter launcher in the transmutation menu will allow you to create a Mk. 4 Scatterpult Launcher. The Mk.4 Scatterpult Launcher has increased range and launches all vials in a narrow cone. The Mk.4 Scatterpult Launcher has 3 vial slots.

Combining a Mk.4 Catapult, Scatter, and Scatterpult Launcher in the transmutation menu will allow you to create a Mk.5 Super Launcher. The Mk.5 Super Launcher has increased range, cooldown, and launches all vials in a narrow cone. Additionally, socketed vials have a +30% wider impact radius. The Mk.5 Super Launcher has 4 vial sockets.

For the different runes in the game, Rahlence has a detailed guide about the different ones.
This guide can be found here - https://steamproxy.net/sharedfiles/filedetails/?id=1911997938