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 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 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 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.

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 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.

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.

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>.

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.

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>.

This package provides a collection of functions that allows for easy and consistent use of environment variables. This includes setting, checking, retrieving, transforming, and validating values stored in environment variables.

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.

This package provides a set of function for clustering data observation with hybrid method Fuzzy ART and K-Means by Sengupta, Ghosh & Dan (2011) <doi:10.1080/0951192X.2011.602362>.

Procedures for calculating variance components, study variation, percent study variation, and percent tolerance for gauge repeatability and reproducibility study. Methods included are ANOVA and Average / Range methods. Requires balanced study.

This package implements a geographically weighted partial correlation which is an extension from gwss() function in the GWmodel package (Percival and Tsutsumida (2017) <doi:10.1553/giscience2017_01_s36>).

Facilitates the analysis and evaluation of hydrologic model output and time-series data with functions focused on comparison of modeled (simulated) and observed data, period-of-record statistics, and trends.