This package provides a differential abundance method for the analysis of microbiome data. radEmu estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) <doi:10.1093/biomet/asag009>.

This package provides methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages rCDK and fingerprint for cheminformatics functionality. Methods for reaction similarity and sub-structure masking are as described in: Giri et al. (2015) <doi:10.1093/bioinformatics/btv416>.

The rankFD() function calculates the Wald-type statistic (WTS) and the ANOVA-type statistic (ATS) for nonparametric factorial designs, e.g., for count, ordinal or score data in a crossed design with an arbitrary number of factors. Brunner, E., Bathke, A. and Konietschke, F. (2018) <doi:10.1007/978-3-030-02914-2>.

The rfacts package is an R interface to the Fixed and Adaptive Clinical Trial Simulator FACTS. It programmatically invokes FACTS to run clinical trial simulations. It aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility.

This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

This package contains data used by pagoda2. The data within this package are the 3000 bone marrow cells used for vignettes.

This package computes cell fate bias for multi-lineage single-cell data. It also provides visualization tools for analyzing these biases.

This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.

This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.

This package provides data sets and functions for Klein and Moeschberger (1997), "Survival Analysis, Techniques for Censored and Truncated Data", Springer.

This package extends the out of memory vectors of ff with statistical functions and other utilities to ease their usage.

This is a pure R implementation of the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) with optional restarts (IPOP-CMA-ES).

DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

Calculates a range of UK freshwater invertebrate biotic indices including BMWP, Whalley, WHPT, Habitat-specific BMWP, AWIC, LIFE and PSI.

This package implements an S3 class based on data.table to store and process efficiently ethomics (high-throughput behavioural) data.

Miscellaneous R functions, including functions related to graphics (mostly for base graphics), permutation tests, running mean/median, and general utilities.

Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.

Flexible tools to fit, tune and obtain absolute risk predictions from regularized cause-specific cox models with elastic-net penalty.

This package provides tools to sort DICOM-format medical image files, and convert them to NIfTI-1 format.

Phase I/II adaptive dose-finding design for combination studies where toxicity rates are supposed to increase with both agents.

This package provides classes and methods for implementing aquatic ecosystem models, for running these models, and for visualizing their results.

This package performs some enhanced variable selection algorithms based on the least absolute shrinkage and selection operator for regression model.