I would like to knowif you know about any R package that allows to find interactions between 2 different gene lists.
After a google search, I didn't find any.
Your post title talks about molecule interactions, but your question refers to gene lists. Could you specify a bit more clearly what it is you're after?
Are you perhaps interested in protein-protein interactions, or?
well actually I have 2 lists with transcript IDs and I want to find interactions between them at all levels: protein-protein interactions, protein-gene interactions,etc