A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.

Using non-parametric tests, naive associations between omics 
    features and metadata in cross-sectional data-sets are detected. In a second 
    step, confounding effects between metadata associated to the same omics 
    feature are detected and labeled using nested post-hoc model comparison
    tests, as first described in 
    Forslund, Chakaroun, Zimmermann-Kogadeeva, et al. (2021) <doi:10.1038/s41586-021-04177-9>. 
    The generated output can be graphically summarized using the built-in plotting function.

High-throughput, flexible and reproducible extraction of data from figures in primary research papers. metaDigitise() can extract data and / or automatically calculate summary statistics for users from box plots, bar plots (e.g., mean and errors), scatter plots and histograms.

Metadynamics is a state of the art biomolecular simulation technique.
  'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
  it possible to perform metadynamics using various simulation codes. The results of
  metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
  'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
  It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
  to calculate a free energy surface from hills. Minima can be located and plotted on
  the free energy surface. Transition states can be analyzed by Nudged Elastic Band
  method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy
  surfaces, minima and transition paths can be plotted to produce publication quality
  images.

Metadynamics is a state of the art biomolecular simulation technique.
  'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes
  it possible to perform metadynamics using various simulation codes. The results of
  metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package
  'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package.
  As an addendum, 'metadynaminer3d' is used to visualize 3D hills. It uses
  a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037>
  to calculate a free energy surface from hills. Minima can be located and plotted on
  the free energy surface. Free energy surfaces and minima can be plotted to produce
  publication quality images.