This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package provides density, distribution, quantile and hazard functions of a stable variate, as well as generalized regression models for the parameters of a stable distribution.

This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.

Perform mediation analysis via the fast-and-robust bootstrap test ROBMED (Alfons, Ates & Groenen, 2022a; <doi:10.1177/1094428121999096>), as well as various other methods. Details on the implementation and code examples can be found in Alfons, Ates, and Groenen (2022b) <doi:10.18637/jss.v103.i13>. Further discussion on robust mediation analysis can be found in Alfons & Schley (2024) <doi:10.31234/osf.io/2hqdy>.

This package provides a convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. reprex also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

Create Tables for Reporting Clinical Trials. Calculates descriptive statistics and hypothesis tests, arranges the results in a table ready for reporting with LaTeX, HTML or Word.

Play casino games in the R console, including poker, blackjack, and a slot machine. Try to build your fortune before you succumb to the gambler's ruin!

This package contains functions to perform copula estimation by the non-parametric Bayesian method, Dirichlet-based Polya Tree. See Ning (2018) <doi:10.1080/00949655.2017.1421194>.

Fast functions for effective sample size, weighted multivariate mean, variance, and quantile computation, and weight diagnostic plot for generic importance sampling type or other probability weighted samples.

This package provides functions to compute generalized eigenvalues and eigenvectors, the generalized Schur decomposition and the generalized Singular Value Decomposition of a matrix pair, using Lapack routines.

Package for Genetic Epidemiologic Methods Developed at MSKCC. It contains functions to calculate haplotype specific odds ratio and the power of two stage design for GWAS studies.

Create a grid-based graphviz using the following functions: 1 - Creating the data.frame where the nodes are; 2 - Adding and editing nodes; 3 - Plotting these nodes.

This package provides methods to perform and analyse I-prior regression models. Estimation is done either via direct optimisation of the log-likelihood or an EM algorithm.

One-way and two-way analysis of variance for replicated point patterns, grouped by one or two classification factors, on the basis of the corresponding K-functions.

Interact with LaminDB'. LaminDB is an open-source data framework for biology. This package allows you to query and download data from LaminDB instances.

This package contains functions for performing Mokken scale analysis on test and questionnaire data. It includes an automated item selection algorithm, and various checks of model assumptions.

Body Shape and related measurements from the US National Health and Nutrition Examination Survey (NHANES, 1999-2004). See http://www.cdc.gov/nchs/nhanes.htm for details.

Implementation for nFunNN method, which is a novel nonlinear functional principal component analysis method using neural networks. The crucial function of this package is nFunNNmodel().

Geospatial data for creating maps of New South Wales (NSW), Australia, and some helpers to work with common problems like normalising postcodes. Registers its data with cartographer'.

Deterministic Pena-Yohai initial estimator for robust S estimators of regression. The procedure is described in detail in Pena, D., & Yohai, V. (1999) <doi:10.2307/2670164>.

Various useful functions for statisticians: describe data, plot Kaplan-Meier curves with numbers of subjects at risk, compare data sets, display spaghetti-plot, build multi-contingency tables...