Software

CRAN

• mxnorm: software for normalizing single-cell multiplex imaging data (CRAN; GitHub;software paper;methodology paper).

• registr

  • R software for registering exponential family functional data (CRAN;GitHub)
  • There are associated papers for Incomplete curve registration and the underlying methodology

• refund: a popular package for regression with functional data which I maintain and contribute to (CRAN; GitHub).

• refund.shiny

  • I developed the refund.shiny package with Jeff Goldsmith. (CRAN; GitHub; paper).

  • Through the plot_shiny() function, this package produces interactive graphics for several of the most common functional data analyses:

    • Functional principal components analysis
    • Multilevel and time-varying functional principal components analysis
    • Function-on-scalar regression
    • Functional linear concurrent regression

  • This package is closely aligned with the refund package: analyses are conducted using functions in refund and return objects that can be plotted using refund.shiny::plot_shiny().

Bioconductor

• VectraPolarisData: An ExperimentHub data package that contain experiment-scale data from two large single-cell multiplex immunofluorescence imaging experiments (Bioconductor; GitHub).

GitHub

• fastGFPCA: fast Generalized Functional Principal Components Analysis.
• mica: Multi Image CDF Alignment, a package for within-subject intensity normalization of structural MRI data.
• depthTests, a package developed with Sara Lopez-Pintado for conducting nonparametric hypothesis tests based on multivariate band depth.