To provide a high dimensional grouped variable selection approach for detection of whole-genome SNP effects and SNP-SNP interactions, as described in Fang et al. (2017, under review).

This package provides a tidy approach to analysis of biological sequences. All processing and data-storage functions are heavily optimized to allow the fastest and most efficient data storage.

Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) <doi:10.1111/2041-210X.14090>.

Utilities for processing input and output files associated with the Raven Hydrological Modelling Framework. Includes various plotting functions, model diagnostics, reading output files into extensible time series format, and support for writing Raven input files. The RavenR package is also archived at Chlumsky et al. (2020) <doi:10.5281/zenodo.4248183>. The Raven Hydrologic Modelling Framework method can be referenced with Craig et al. (2020) <doi:10.1016/j.envsoft.2020.104728>.

Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.

R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data.

This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.

Inspired by the the futile.logger R package and logging Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.

This package provides a ggplot2 extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.

This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.

This package lets you manage configuration values across multiple environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value.

The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.

This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.

Save MultiAssayExperiments to h5mu files supported by muon and mudata. Muon is a Python framework for multimodal omics data analysis. It uses an HDF5-based format for data storage.

Data files and functions accompanying the book Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt (2015) "Bayesian Data Analysis in Ecology using R, BUGS and Stan", Elsevier, New York.

This package implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2022) <doi:10.1111/biom.13465> for transformation-free linear regression for compositional outcomes and predictors.

This package performs reference based multiple imputation of recurrent event data based on a negative binomial regression model, as described by Keene et al (2014) <doi:10.1002/pst.1624>.

Calculates various estimates for measures of educational differentials, the relative importance of primary and secondary effects in the creation of such differentials and compares the estimates obtained from two datasets.

Multivariate Gaussian mixture model with a determinant point process prior to promote the discovery of parsimonious components from observed data. See Xu, Mueller, Telesca (2016) <doi:10.1111/biom.12482>.

This package provides computational methods for detecting adverse high-order drug interactions from individual case safety reports using statistical techniques, allowing the exploration of higher-order interactions among drug cocktails.