Q:
I have been searching for a bioinformatics software package that allows for the integration of different NGS analysis, RNA-Seq, HiC, ChIP-Seq in one project.

Does software like this exist yet?

A:
I don’t know of a package that can exactly help you but in some of previous work we’ve integrated RNA-seq and Chip-seq.

See links:

http://papers.gersteinlab.org/papers/worm_HM/
http://papers.gersteinlab.org/papers/tfmodel/