Visualise admixture as pie charts on a projected map, admixture as traditional structure barplots or facet barplots, and scatter plots from genotype principal components analysis. A shiny app allows users to create admixture maps interactively. Jenkins TL (2024) <doi:10.1111/1755-0998.13943>.

Implementations of various control theory methods for use in brain and psychological networks. Contains controllability statistics from Pasqualetti, Zampieri & Bullo (2014) <doi:10.1109/TCNS.2014.2310254>, optimal control algorithms from Lewis, Vrabie & Syrmos (2012, ISBN:978-0-470-63349-6), and various utilities.

Oblique random survival forests incorporate linear combinations of input variables into random survival forests (Ishwaran, 2008 <DOI:10.1214/08-AOAS169>). Regularized Cox proportional hazard models (Simon, 2016 <DOI:10.18637/jss.v039.i05>) are used to identify optimal linear combinations of input variables.

Data sets and functions used in the polish book "Przewodnik po pakiecie R" (The Hitchhiker's Guide to the R). See more at <http://biecek.pl/R>. Among others you will find here data about housing prices, cancer patients, running times and many others.

GUI for entering test items and obtaining raw and transformed scores. The results are shown on the console and can be saved to a tabular text file for further statistical analysis. The user can define his own tests and scoring procedures through a GUI.

This package provides S3 generic methods and some default implementations for Bayesian analyses that generate Markov Chain Monte Carlo (MCMC) samples. The purpose of universals is to reduce package dependencies and conflicts. The nlist package implements many of the methods for its nlist class.

Vega and Vega-Lite parse text in JSON notation to render chart-specifications into HTML'. This package is used to facilitate the rendering. It also provides a means to interact with signals, events, and datasets in a Vega chart using JavaScript or Shiny'.

Turn R analysis outputs into full sentences, by writing vectors into in-sentence lists, pluralising words conditionally, spelling out numbers if they are at the start of sentences, writing out dates in full following US or UK style, and managing capitalisations in tidy data.

This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.

This package implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.

This collection of utilities contains tooling and templates to assist in creating releases on GitHub and publishing them on PyPI. It is designed to be used by Robot Framework and tools and libraries in its ecosystem, but can naturally be used also by other projects.

This package provides a trimmed down copy of the "kent-core source tree" turned into a C library for manipulation of .2bit files. See <https://genome.ucsc.edu/FAQ/FAQformat.html#format7> for a quick overview of the 2bit format. The "kent-core source tree" can be found here: <https://github.com/ucscGenomeBrowser/kent-core/>. Only the .c and .h files from the source tree that are related to manipulation of .2bit files were kept. Note that the package is primarily useful to developers of other R packages who wish to use the 2bit C library in their own C'/'C++ code.

This package provides a collection of programs for plotting SKEW-T,log p diagrams and wind profiles for data collected by radiosondes (the typical weather balloon-borne instrument). The format of this plot with companion lines to assess atmospheric stability are both standard in meteorology and difficult to create from basic graphics functions. Hence this package. One novel feature is being able add several profiles to the same plot for comparison. Use "help(ExampleSonde)" for an explanation of the variables needed and how they should be named in a data frame. See <https://github.com/dnychka/Radiosonde> for the package home page.

An optimized method for identifying mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson-Binomial distribution that takes into account that some samples are more mutated than others. See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels. (2016) "A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>]. The mutations matrices are sparse matrices. The method developed takes advantage of the advantages of this type of matrix to save time and computing resources.

New Markov chain Monte Carlo (MCMC) samplers new to be thoroughly tested and their performance accurately assessed. This requires densities that offer challenging properties to the novel sampling algorithms. One such popular problem is the Rosenbrock function. However, while its shape lends itself well to a benchmark problem, no codified multivariate expansion of the density exists. We have developed an extension to this class of distributions and supplied densities and direct sampler functions to assess the performance of novel MCMC algorithms. The functions are introduced in "An n-dimensional Rosenbrock Distribution for MCMC Testing" by Pagani, Wiegand and Nadarajah (2019) <arXiv:1903.09556>.

An ASCII ruler is for measuring text and is especially useful for sequence analysis. Included in this package are methods to create ASCII rulers and associated GenBank sequence blocks, multi-column text displays that make it easy for viewers to locate nucleotides by position.

This package implements methods for sample size reduction within Linear and Quadratic Discriminant Analysis in Lapanowski and Gaynanova (2020) <arXiv:2005.03858>. Also includes methods for non-linear discriminant analysis with simultaneous sparse feature selection in Lapanowski and Gaynanova (2019) PMLR 89:1704-1713.

This package provides a disk-based data manipulation tool for working with large-than-RAM datasets. Aims to lower the barrier-to-entry for manipulating large datasets by adhering closely to popular and familiar data manipulation paradigms like dplyr verbs and data.table syntax.

Flexible and efficient cleaning of data with interactivity. datacleanr facilitates best practices in data analyses and reproducibility with built-in features and by translating interactive/manual operations to code. The package is designed for interoperability, and so seamlessly fits into reproducible analyses pipelines in R'.

This package provides methods for efficient algebraic operations and factorization of dyadic matrices using Rcpp and RcppArmadillo'. The details of dyadic matrices and the corresponding methodology are described in Kos, M., Podgórski, K., and Wu, H. (2025) <doi:10.48550/arXiv.2505.08144>.

The goal of forstringr is to enable complex string manipulation in R especially to those more familiar with LEFT(), RIGHT(), and MID() functions in Microsoft Excel. The package combines the power of stringr with other manipulation packages such as dplyr and tidyr'.

Graph clustering using an agglomerative algorithm to maximize the integrated classification likelihood criterion and a mixture of stochastic block models. The method is described in the article "Model-based clustering of multiple networks with a hierarchical algorithm" by T. Rebafka (2022) <arXiv:2211.02314>.

This package provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class incidence2 is used to store computed incidence and can be easily manipulated, subsetted, and plotted.

This is an extension package to logrx', which is a log creation program focused on Clinical Reporting within the Pharma Industry. This package enables a simple shiny-based Add-in that provides a point and click interface to produce a log for a single program.