Performs Penalized Multivariate Analysis: a penalized
        matrix decomposition, sparse principal components analysis,
        and sparse canonical correlation analysis, described in
        Witten, Tibshirani and Hastie (2009)
        <doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani
        (2009) Extensions of sparse canonical correlation analysis,
        with applications to genomic data
        <doi:10.2202/1544-6115.1470>.

We innovatively defined a pathway mutation accumulate perturbation score (PMAPscore) to reflect the position and the cumulative effect of the genetic mutations at the pathway level. Based on the PMAPscore of pathways, identified prognosis-related pathways altered by somatic mutation and predict immunotherapy efficacy by constructing a multiple-pathway-based risk model (Tarca, Adi Laurentiu et al (2008) <doi:10.1093/bioinformatics/btn577>).

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups.  Implements methods described in:  Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>.  Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>.  Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>.  Matzke et al. (2013) <doi:10.1002/pmic.201200269>.  Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>.  Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Monte Carlo based model choice for applied phylogenetics of
    continuous traits. Method described in  Carl Boettiger, Graham Coop,
    Peter Ralph (2012) Is your phylogeny informative? Measuring
    the power of comparative methods, Evolution 66 (7)
    2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.