To incorporate neighbor genotypic identity into genome-wide association studies, the package provides a set of functions for variation partitioning and association mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1038/s41437-020-00401-w>.

To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.

An implementation of a method based on information theory devised 
    for the identification of genes showing a significant variation of expression
    across multiple conditions. Given expression estimates from any number of 
    RNA-Seq samples and conditions it identifies genes or transcripts with a 
    significant variation of expression across all the conditions studied, 
    together with the samples in which they are over- or under-expressed. 
    Zambelli et al. (2018) <doi:10.1093/nar/gky055>.

Within this package the XML-RPC API to NEOS <https://neos-server.org/neos/> is implemented. This enables the user to pass optimization problems to NEOS and retrieve results within R.

Determine the number of dimensions to retain in exploratory factor analysis. The main function, nest(), returns the solution and the plot(nest()) returns a plot.

Provides functions to compute the modularity and modularity-related roles in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 2005, <doi:10.1038/nature03288>).

An interface to the 'NetCDF' file formats designed by Unidata
  for efficient storage of array-oriented scientific data and descriptions.
  Most capabilities of 'NetCDF' version 4 are supported. Optional conversions
  of time units are enabled by 'UDUNITS' version 2, also from Unidata.

Interface to use and access Wilensky's 'NetLogo' (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the 'NetLogo' 'Mathematica' Link <https://github.com/NetLogo/Mathematica-Link>.