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Bioconductor: open software development for computational biology and bioinformatics
Details of the aims and methods of Bioconductor, the collaborative creation of extensible software for computational biology and bioinformatics, and current challenges are described.
Unbiased Recursive Partitioning: A Conditional Inference Framework
A unified framework for recursive partitioning is proposed which embeds tree-structured regression models into a well defined theory of conditional inference procedures and it is shown that the predicted accuracy of trees with early stopping is equivalent to the prediction accuracy of pruned trees with unbiased variable selection.
kernlab - An S4 Package for Kernel Methods in R
The package contains dot product primitives (kernels), implementations of support vector machines and the relevance vector machine, Gaussian processes, a ranking algorithm, kernel PCA, kernel CCA, and a spectral clustering algorithm.
Implementing a Class of Permutation Tests: The coin Package
A computational framework is established in coin that likewise embeds the corresponding R functionality in a common S4 class structure with associated generic functions, inherit the flexibility of the underlying theory and conditional inference functions for important special cases can be set up easily.
topicmodels: An R Package for Fitting Topic Models
The R package topicmodels provides basic infrastructure for fitting topic models based on data structures from the text mining package tm to estimate the similarity between documents as well as between a set of specified keywords using an additional layer of latent variables.
Model-Based Recursive Partitioning
An algorithm for model-based recursive partitioning is suggested that yields a partitioned (or segmented) parametric model that can be effectively visualized and that subject-matter scientists are used to analyzing and interpreting.