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.

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>.

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

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

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

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

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

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

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.

This package implements the Enhanced Portfolio Optimization (EPO) method as described in Pedersen, Babu and Levine (2021) <doi:10.2139/ssrn.3530390>.

Modelizations and previsions functions for Functional AutoRegressive processes using nonparametric methods: functional kernel, estimation of the covariance operator in a subspace, ...

This package provides functions to explore datasets from the Global Biodiversity Information Facility (GBIF - <https://www.gbif.org/>) using a Shiny interface.

This package implements an S7 class for estimates based on influence functions, with forward mode automatic differentiation defined for standard arithmetic operations.

Lexical response data is a package that can be used for processing cued-recall, free-recall, and sentence responses from memory experiments.

Sampling and evaluation methods to apply Monetary Unit Sampling (or in older literature Dollar Unit Sampling) during an audit of financial statements.

Draw nested extreme value random variables, which are the variables that appear in the latent variable formulation of the nested logit model.

Estimates (and controls for) phylogenetic signal through phylogenetic eigenvectors regression (PVR) and phylogenetic signal-representation (PSR) curve, along with some plot utilities.