Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (<DOI:10.1111/1755-0998.12665>) for more information.

This package implements the s-values proposed by Ed. Leamer. It provides a context-minimal approach for sensitivity analysis using extreme bounds to assess the sturdiness of regression coefficients.

Simple utilities to generate a Dockerfile from a directory or project, build the corresponding Docker image, push the image to DockerHub, and publicly share the project via Binder.

Historical voting data of the United Nations General Assembly. This includes votes for each country in each roll call, as well as descriptions and topic classifications for each vote.

This package provides a collection of functions for computing "r-values" from various kinds of user input such as MCMC output or a list of effect size estimates and associated standard errors. Given a large collection of measurement units, the r-value, r, of a particular unit is a reported percentile that may be interpreted as the smallest percentile at which the unit should be placed in the top r-fraction of units.

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

This package provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.

This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".

This package provides a generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. It can also handle clustered categorical responses.

The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".

This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications.

This package provides functions for regulation, decomposition and analysis of space-time series. The pastecs library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R.

This package is for analysis of SILAC labeled complexome profiling data. It uses peptide table in tab-delimited format as an input and produces ready-to-use tables and plots.

This package provides a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).

Smooth quantile normalization is a generalization of quantile normalization, which is average of the two types of assumptions about the data generation process: quantile normalization and quantile normalization between groups.

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

This package implements Roy's bivariate geometric model (Roy (1993) <doi:10.1006/jmva.1993.1065>): joint probability mass function, distribution function, survival function, random generation, parameter estimation, and more.

This package provides a GUI with which users can construct and interact with Canonical Correspondence Analysis and Canonical Non-Symmetrical Correspondence Analysis and provides inferential results by using Bootstrap Methods.

This package implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package config'.

Statistical modeling for correlated count data using the beta-binomial distribution, described in Martin et al. (2020) <doi:10.1214/19-AOAS1283>. It allows for both mean and overdispersion covariates.

This package performs generalized Susceptible-Exposed-Infected-Recovered (SEIR) modeling to predict epidemic curves. The method is described in Peng et al. (2020) <doi:10.1101/2020.02.16.20023465>.

This package provides utilities for encoding and decoding coordinates to/from Hilbert curves based on the iterative encoding implementation described in Chen et al. (2006) <doi:10.1002/spe.793>.