A mathematical optimization procedure in combination with statistical bootstrap for the estimation of the latent signals (sometimes called scores) informing the global consensus ranking (often named aggregation ranking). To solve mid/large-scale problems, users should install the 'gurobi' optimiser (available from <https://www.gurobi.com/>).

Set of hydrological functions including an R
        implementation of the hydrological model TOPMODEL, which is
        based on the 1995 FORTRAN version by Keith Beven. From version
        0.7.0, the package is put into maintenance mode.

A toolkit for calculating topographic distances and identifying and plotting topographic paths. Topographic distances can be calculated along shortest topographic paths (Wang (2009) <doi:10.1111/j.1365-294X.2009.04338.x>), weighted topographic paths (Zhan et al. (1993) <doi:10.1007/3-540-57207-4_29>), and topographic least cost paths (Wang and Summers (2010) <doi:10.1111/j.1365-294X.2009.04465.x>). Functions can map topographic paths on colored or hill shade maps and plot topographic cross sections (elevation profiles) for the paths.

Using Gaussian graphical models we propose a novel approach to
             perform pathway analysis using gene expression. Given the
             structure of a graph (a pathway) we introduce two statistical
             tests to compare the mean and the concentration matrices between
             two groups. Specifically, these tests can be performed on the
             graph and on its connected components (cliques). The package is
             based on the method described in Massa M.S., Chiogna M., Romualdi
             C. (2010) <doi:10.1186/1752-0509-4-121>.

Flexible and ergonomic topological sorting implementation for
    R. Supports a variety of input data encoding (lists of edges or
    adjacency matrices, graphs edge direction), stable sort variants as
    well as cycle detection with detailed diagnosis.

A collection of functions for visualizing,exploring and annotating genetic association results.Association results from multiple traits can be viewed simultaneously along with gene annotation, over the entire genome (Manhattan plot) or in the more detailed regional view.