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Hey dakka dakka, for a while now I've been contemplating the idea of a 40k Skaven army. These guys will pretty much be my interpretation of space age Skaven from WHFB so my apologies to all you pro-Hrud'ers out there
I really like the WHFB Skaven however I have little interest in the game so I thought to instead convert an army of Skaven to represent (or 'count as' if you will) a particular 40k army w or w/o an allied detachment.
I'd really like to include allies to give the army a unique feel to them and to give me an opportunity to further explore the various factions.

I have thought about Tyranids, Nurgle Marines w/Nurgle Daemons, Imperial Guard, Dark Eldar, Orks, even Necrons

My goal is to analyse the technology of the WHFB Skaven and essentially 'evolve' it to appear capable and relevant to 40k.
An excellent example of what I'm trying to achieve is Ikit Claw. Asthetically they will be more in-keeping with the whole Grimdark deal

I really love the look of this model and it is a big source of inspiration for this idea
Once I've decided on an army to base them around I can begin planning conversions and exploring new ideas.

One last thing, would someone be able to clarify exactly how Allied Detachments work? I've heard people scrutinise the system and while this will be a largely fluffy army I'd like it to not fall apart on the battlefield.

Anyway, let me know what codex you think would work for Space Skaven
Cheers

Depends on which part of the skaven you want to highlight the most.

Klan Skyre = Orks; lot's of wacky technology with high damage, but a good chance to damage yourself as well

Klan Eshin = Eldar/Dark Eldar; quick, with lot's of "underhanded" tactics

Breeder Clan = (DarkAngels?), Eldar; Lot's of durable modells


Personally I would chose Eldar, because they can field relatively good amount of cheap bodies, monstrous creatures, and technological advanced thingamajigs.

Have you tried renegade militia? They're like imperial guard but with tweaks to make them more ragtag and evil [just like skaven].

Ya know, Necrons would be a funny idea. Their vehicles are all funky and crazy looking and the "Resurrection Protocols" rule could be interpreted as more rats arrive to reenforce them they are so many, you kill one, 2 more pop out

Eldar/Dark Eldar would be a good combination as Drunk Philisoph pointed out.
Fast, precise strikes and poisoned attacks make sense as well as stealth capabilities plus Dark Eldar take slaves like skaven. There isn't much in the way of plague options (as far as I'm aware)
I'm also thinking about it now I'd love to field them with lots of regular rats as units. Be them Nurglings, Rippers, Scarabs or Grots.

I do not have much experience with 40k armies outside of SM so further ideas and suggestions are more than welcome

IG are by far the best way (In my opinion) to field skaven in 40k
Conscripts as slaves, Regular Skaven as guardsmen, Ogryns as Rat Ogres, Weapon Teams as Heavy Weapon Teams, The list goes on.
It's as perfect a fit as you're going to get.

You could make an argument for using almost any army as Space Skaven. Imperial Guard would give you the hordes of cheaply armed infantry, with some big and strong vehicles. Chaos can do the same, with lots of cultists. Necrons would give you the hordes of well armed infantry (and Tesla weapons would be fluffy for Skaven). Orks would give you the hordes of close combat infantry with the scavenged vehicles.

By the way, if you weren't aware, Mantic makes Space Skaven models.
http://www.manticgames.com/Shop-Home/Warpath/Veer-myn.html

To answer your other question (the one about allies) the way it works is you can take units from a second codex. The FOC for allies has fewer slots so you are unable to take as many units.