Nucleosome positioning for Tiling Arrays and NGS experiments.

Estimates VAR and VARX models with Structured Penalties.

Dynamic simulations and graphical depictions of autoregressive relationships.

Probability distributions that are sometimes useful in hydrology.

Tabulate and plot directional and other multivariate histograms.

Generalise the starting point of the array index.

Tokenizes a string that represents a regular expression.

This tool provides an algorithm to identify rare cell types in single-cell data. It also identifies abundant cell types. The method is based on transcript counts obtained with unique molecular identifies.

Eprime is a set of programs for administering psychological experiments by computer. This package provides functions for loading, parsing, filtering and exporting data in the text files produced by Eprime experiments.

Non-inferiority test and diagnostic test are very important in clinical trails. This package is to get a p value from the non-inferiority test for ROC curves from diagnostic test.

This package provides a tool to exchange data between R and Raven sound analysis software (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package warbleR'.

An implementation of algorithms for estimation of the graphical lasso regularization parameter described in Pedro Cisneros-Velarde, Alexander Petersen and Sang-Yun Oh (2020) <http://proceedings.mlr.press/v108/cisneros20a.html>.

Perform derivative-free optimization algorithms in R using C++. A wrapper interface is provided to call C function of the bobyqa implementation (See <https://github.com/emmt/Algorithms/tree/master/bobyqa>).

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.

This package performs regularization of differential item functioning (DIF) parameters in item response theory (IRT) models (Belzak & Bauer, 2020) <https://pubmed.ncbi.nlm.nih.gov/31916799/> using a penalized expectation-maximization algorithm.

This package implements diversification analyses using the phylogenetic birth-death-shift model. It leverages belief propagation techniques to calculate branch-specific diversification rates, see Kopperud & Hoehna (2025) <doi:10.1093/sysbio/syaf041>.

Execute FOCAL (<https://en.wikipedia.org/wiki/FOCAL_(programming_language)>) source code directly in R'. This is achieved by translating FOCAL code into equivalent R commands and controlling the sequence of execution.

An extremely simple stack data type, implemented with R6 classes. The size of the stack increases as needed, and the amortized time complexity is O(1). The stack may contain arbitrary objects.

This package provides an interface for the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This includes interfaces to blastn, blastp, blastx, and makeblastdb.

This package provides functions for bitwise operations on integer vectors.

Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.

MS-based metabolomics data processing and compound annotation pipeline.

Pipeline for the anaysis of a MS-GBS experiment.

This package provides tools to analyze binary graph objects.