I am really new here and do not know much and I was wondering what the items are used for. Which ones should I keep and which ones should I sell. I am running out of space in my warehouse! 

I know that wood and stone are used for buildings and I need vermillion to research genes. But what about rubies? Shells and marbles? Or how about Laminaria, lazurites and cotton?

I looked in the guides section, but I couldn't find anything helpful.

I hope my question makes sense :)

Under the Help tab you will find a list of recipes, this shows you all the things you can create, and what materials they require.
There's also the odd alternate use - such as the marketplace during exploring, which exchanges a couple of units from one random material into another, or buildings which allow you to reroll one color gene, or allow you to enable one more breeding on your pet, for a fee of some silver and some gems (at least, they've been gems for me so far.)

Thank you! I never noticed the list of recipes