several R packages and matlab functions (such as k-means)
what is the dimensions of your data (how many observations and covariates)
There are some workflows built into Partek GS software that can integrate SNP array and expression array data. I haven't used PGS in quite some time, so there are probably newer versions available with newer workflows. Unfortunately, the software isn't free and I don't know of any specific R packages for such integrated analysis.
Partek GS is not updated with new functions since 3 years at least. Anyway, if for "co-clustering" Shayan means any kind of co-occurrence analysis, there is not need here for Partek. Maybe, the aim should be better explained here.
see the blockcluster R package:
https://cran.r-project.org/web/packages/blockcluster/vignettes/blockcluster_tutorial.pdf
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