BUS-package: For network reconstruction.
In BUS: Gene network reconstruction

This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical). [Function: BUS]

Both associations can be computed via correlation or mutual information (MI). [Functions: gene.similarity (gene-gene associations) and gene.trait.similarity (gene-trait associations)]

Statistical significance of the association is computed for single and multiple hypotheses testing, using random permutations method [Functions: gene.pvalue, gene.trait.pvalue]

The package can handle data with missing values using bootstrapping methods to fill NAs. [Arguments: na.replica]