This package performs Zoom-Focus Algorithm (ZFA) to optimize testing regions for rare variant association tests in exome sequencing data.

Estimates the rearranged dependence measure ('RDM') of two continuous random variables for different underlying measures. Furthermore, it provides a method to estimate the (SI)-rearrangement copula using empirical checkerboard copulas. It is based on the theoretical results presented in Strothmann et al. (2022) <arXiv:2201.03329> and Strothmann (2021) <doi:10.17877/DE290R-22733>.

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

Solves the individual bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass; Brigolin et al., 2014 <doi:10.3354/aei00093>) and shellfish (Mussel and Clam; Brigolin et al., 2009 <doi:10.1016/j.ecss.2009.01.029>; Solidoro et al., 2000 <doi:10.3354/meps199137>). Allows for spatialized model runs and population simulations.

This package provides basic infrastructure and some algorithms for the traveling salesperson problem(TSP) (also known as the traveling salesman problem).

This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data.

This is a package for Bayesian model averaging and variable selection for linear models, generalized linear models and survival models (cox regression).

This package runs a minimum-hypergeometric (mHG) test as described in "Discovering Motifs in Ranked Lists of DNA Sequences" by Eran Eden.

This package creates lots of colorful plots in a multitude of variations. Try a demo of the LSD by running demotour().

HVP is a quantitative batch effect metric that estimates the proportion of variance associated with batch effects in a data set.

This package implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.

Computation of the EQL for a given family of variance functions, Saddlepoint-approximations and related auxiliary functions (e.g. Hermite polynomials).

Work with configs with a source precedence. Either create own R6 instance or work with convenient functions at a package level.

Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.

This package provides a collection of Item Response Theory (IRT) and Computerized Adaptive Testing (CAT) functions that are used in psychometrics.

Nonparametric estimation and inference for natural direct and indirect effects by Chan, Imai, Yam and Zhang (2016) <arXiv:1601.03501>.

Determines networks of significant synchronization between the discrete states of nodes; see Tumminello et al <doi:10.1371/journal.pone.0017994>.

Interface for creation of slp class smoother objects for use in Generalized Additive Models (as implemented by packages gam and mgcv').

An open-access tool/framework that constitutes the core functions to analyze terrestrial water cycle data across various spatio-temporal scales.

Computes the ridge partial correlation coefficients in a high or ultra-high dimensional linear regression problem. An extended Bayesian information criterion is also implemented for variable selection. Users provide the matrix of covariates as a usual dense matrix or a sparse matrix stored in a compressed sparse column format. Detail of the method is given in the manual.

The r-abd package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter.

This package provides an easy to use library to setup, apply and make inference with discrete time and discrete space hidden Markov models.

This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.

This package provides support for linear order and unimodal order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables.