Provides six modules for tumor microenvironment (TME)
    analysis based on multi-omics data. These modules cover data
    preprocessing, TME estimation, TME infiltrating patterns, cellular
    interactions, genome and TME interaction, and visualization for TME
    relevant features, as well as modelling based on key features. It
    integrates multiple microenvironmental analysis algorithms and
    signature estimation methods, simplifying the analysis and downstream
    visualization of the TME. In addition to providing a quick and easy
    way to construct gene signatures from single-cell RNA-seq data, it
    also provides a way to construct a reference matrix for TME
    deconvolution from single-cell RNA-seq data. The analysis pipeline and
    feature visualization are user-friendly and provide a comprehensive
    description of the complex TME, offering insights into tumour-immune
    interactions (Zeng D, et al. (2024)
    <doi:10.1016/j.crmeth.2024.100910>.  Fang Y, et al. (2025)
    <doi:10.1002/mdr2.70001>).

Addresses the 'log of zero' by developing a new family of 
    estimators called iterated Ordinary Least Squares. 
    This family nests standard approaches such as log-linear and 
    Poisson regressions, offers several computational advantages, 
    and corresponds to the correct way to perform the popular 
    log(Y + 1) transformation. For more details about how to use it, 
    see the notebook at: <https://www.davidbenatia.com/>.

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.

Network functionalities specialized for data generated from input-output tables.

Pre-processing and basic analytical tasks for working with 
    Eurostat's symmetric input–output tables, and basic input–output 
    economics calculations. Part of rOpenGov <https://ropengov.github.io/> 
    for open source open government initiatives.