Can I use the texts in my paper for bioconductor? My group has published a paper to a journal (Natural Methods). Now, I'd like to dump the text in the paper for my R-package vignette and user-manual (bioconductor). 

Can I do it without reference our group's own paper? Or do I have to reference the journal? Does the journal hold the copyright for the published materials?
The customary way to do this is to refer in the manual to the paper.

You are probably not allowed to copy-paste the text of the published paper. If you are concerned about the paywall, many journals allow you to use/distribute the manuscript which you submitted to the journal (prior to editing) - but you should verify this first for Nature Methods.