Regression Models in Systems Biology with R
- Simple Linear Regression PDF
- General Linear Model PDF
- Generalized Linear Model PDF
- Appendix Regression PDF
The Expectation - Maximization algorithm
- The general scheme PDF
- One-dimensional Gaussian mixtures PDF
- Multi-dimensional Gaussian mixtures PDF
Hidden Markov Models
- Markov chains, Likelihood Ratio Test PDF
- The Hidden Markov Model: transition and emission probabilities PDF
- Decoding: the Viterbi algorithm PDF
- Forward algorithm, backward algorithm and posterior probabilities PDF
- Parameter estimation for Hidden Markov Models PDF
- The EM algorithm for Hidden Markov Models PDF
- Example: EM algorithm for Hidden Markov Models HTML
- A Continuous Density Hidden Markov Model examined using R HTML
Classification: Support Vector Machines
- Introduction to SVM models: coming soon
- Additional material - Extreme values of functions with constraints:
HTML
- SVM R-Shiny application: Shiny-APP
- Example data sets:
- Training data: TXT (note that ID’s
are added, this is mandatory!)
- Test data: TXT
- True classes: TXT
- Example model: RDATA
- Example prediction: TXT
- Example tuning data: RDATA
Decision Trees and Random Forest
- Decision Trees PDF
- Example Decision Tree model HTML
- Identification of longevity biomarkers by Random Forest analysis PDF
The RMThreshold R-package
- Short introduction PDF
- Reference manual PDF
- Important notes PDF
- CRAN link
The EMT R-package
- Exact Multinomial Test
- CRAN link
- Example: coming soon
The CCP R-package
- Significance tests for canonical correlation analysis
- CRAN link
- Example: coming soon
Bayesian Statistics
- Bayesian statistics - Can we count on it? PDF
- table game simulation HTML
Dynamics & Nonlinearity
- Hypothesized Bifurcation in the TOR pathway PDF
Other algorithms
- The Metropolis-Hastings Algorithm: coming soon
- Optimization in R: coming later
Multivariate Statistics
- R-Shiny application for bootstrapping and other multivariate
methods: Shiny-APP
- Example data files:
Help me improve this site: uwe.menzel@matstat.org