Store persistent and synchronized data from shiny inputs within the browser. Refresh shiny applications and preserve user-inputs over multiple sessions. A database-like storage format is implemented using Dexie.js <https://dexie.org>, a minimal wrapper for IndexedDB'. Transfer browser link parameters to shiny input or output values. Store app visitor views, likes and followers.

Collection of Xenium spatial transcriptomics datasets provided by 10x Genomics, formatted into the Bioconductor classes, the SpatialExperiment or SpatialFeatureExperiment (SFE), to facilitate seamless integration into various applications, including examples, demonstrations, and tutorials. The constructed data objects include gene expression profiles, per-transcript location data, centroid, segmentation boundaries (e.g., cell or nucleus boundaries), and image.

HTTP::Cookie is a Ruby library to handle HTTP Cookies based on RFC 6265. It has been designed with security, standards compliance and compatibility in mind, to behave just the same as today's major web browsers. It has built-in support for the legacy cookies.txt and cookies.sqlite formats of Mozilla Firefox.

This package provides functions to create confidence intervals for ratios of Poisson rates under misclassification using double sampling. Implementations of the methods described in Kahle, D., P. Young, B. Greer, and D. Young (2016). "Confidence Intervals for the Ratio of Two Poisson Rates Under One-Way Differential Misclassification Using Double Sampling." Computational Statistics & Data Analysis, 95:122â 132.

Fit Thurstonian Item Response Theory (IRT) models in R. This package supports fitting Thurstonian IRT models and its extensions using Stan', lavaan', or Mplus for the model estimation. Functionality for extracting results, making predictions, and simulating data is provided as well. References: Brown & Maydeu-Olivares (2011) <doi:10.1177/0013164410375112>; Bürkner et al. (2019) <doi:10.1177/0013164419832063>.

Extends the test-based Bayes factor (TBF) methodology to multinomial regression models and discrete time-to-event models with competing risks. The TBF methodology has been well developed and implemented for the generalised linear model [Held et al. (2015) <doi:10.1214/14-STS510>] and for the Cox model [Held et al. (2016) <doi:10.1002/sim.7089>].

Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

This package provides tools to create and manipulate probability distributions using S3. Generics pdf(), cdf(), quantile(), and random() provide replacements for base R's d/p/q/r style functions. Functions and arguments have been named carefully to minimize confusion for students in intro stats courses. The documentation for each distribution contains detailed mathematical notes.

This package provides a tool to calculate and plot estimates from models in which an interaction between the main predictor and a continuous covariate has been specified. Methods used in the package refer to Harrell Jr FE (2015, ISBN:9783319330396); Durrleman S, Simon R. (1989) <doi:10.1002/sim.4780080504>; Greenland S. (1995) <doi:10.1097/00001648-199507000-00005>.

Converts video files to mp3', merges multiple audio files and trims audio files using FFmpeg', which is dynamically downloaded to avoid bundling any third-party binaries. Users must ensure compliance with the license terms of FFmpeg when using the package. See <https://github.com/BtbN/FFmpeg-Builds/releases/download/latest/ffmpeg-master-latest-win64-gpl.zip> for details.

Fits Bayesian mixture models to estimate marker dosage for dominant markers in autopolyploids using JAGS (1.0 or greater) as outlined in Baker et al "Bayesian estimation of marker dosage in sugarcane and other autopolyploids" (2010, <doi:10.1007/s00122-010-1283-z>). May be used in conjunction with polySegratio for simulation studies and comparison with standard methods.

This package implements target trial emulation methods to apply randomized clinical trial design and analysis in an observational setting. Using marginal structural models, it can estimate intention-to-treat and per-protocol effects in emulated trials using electronic health records. A description and application of the method can be found in Danaei et al (2013) <doi:10.1177/0962280211403603>.

U-Boot is a bootloader used mostly for ARM boards. It also initializes the boards (RAM etc).

It allows network booting and uses the device-tree from the firmware, allowing the usage of overlays. It can act as an EFI firmware for the grub-efi-netboot-removable-bootloader. This is a 32-bit build of U-Boot.

Datasets to be used primarily in conjunction with Ascent training materials but also for the book SAMS Teach Yourself R in 24 Hours (ISBN: 978-0-672-33848-9). Version 1.0-7 is largely for use with the book; however, version 1.1 has a much greater focus on use with training materials, whilst retaining compatibility with the book.

Includes several classifications such as International Statistical Classification of Diseases and Related Health Problems 10th Revision (ICD10), Anatomical Therapeutic Chemical (ATC) Classification, The International Classification of Diseases for Oncology (ICD-O-3), and International Classification of Primary Care (ICPC). Includes function that adds descriptive label to code value. Depending on classification following languages are available: English, Finnish, Swedish, and Latin.

This package provides a collection of coding functions as alternatives to the standard functions in the stats package, which have names starting with contr.'. Their main advantage is that they provide a consistent method for defining marginal effects in factorial models. In a simple one-way ANOVA model the intercept term is always the simple average of the class means.

This package provides a novel integral estimator for estimating the causal effects with continuous treatments (or dose-response curves) and a localized derivative estimator for estimating the derivative effects. The inference on the dose-response curve and its derivative is conducted via nonparametric bootstrap. The reference paper is Zhang, Chen, and Giessing (2024) <doi:10.48550/arXiv.2405.09003>.

This package provides new layer functions to tmap for creating various types of cartograms. A cartogram is a type of thematic map in which geographic areas are resized or distorted based on a quantitative variable, such as population. The goal is to make the area sizes proportional to the selected variable while preserving geographic positions as much as possible.

This package provides a simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. It can also be used for differential expression/2-class data.

The form() subroutine may be exported from the module. It takes a series of format (or "picture") strings followed by replacement values, interpolates those values into each picture string, and returns the result. The effect is similar to the inbuilt perl format mechanism, although the field specification syntax is simpler and some of the formatting behaviour is more sophisticated.

This package provides tools for applying the Bayesian Gower agreement methodology (presented in the package vignette) to nominal or ordinal data. The framework can accommodate any number of units, any number of coders, and missingness; and can handle both one-way and two-way random study designs. Influential units and/or coders can be identified easily using leave-one-out statistics.

Model selection and averaging for regression, generalized linear models, generalized additive models, graphical models and mixtures, focusing on Bayesian model selection and information criteria (Bayesian information criterion etc.). See Rossell (2025) <doi:10.5281/zenodo.17119597> (see the URL field below for its URL) for a hands-on book describing the methods, examples and suggested citations if you use the package.

This package implements simulated tests for the hypothesis that terminal digits are uniformly distributed (chi-squared goodness-of-fit) and the hypothesis that terminal digits are independent from preceding digits (several tests of independence for r x c contingency tables). Also, for a number of distributions, implements Monte Carlo simulations for type I errors and power for the test of independence.

This package provides S4 generic functions modeled after the matrixStats API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.