Implementation of commonly used p-value-based and parametric multiple testing procedures (computation of adjusted p-values and simultaneous confidence intervals) and parallel gatekeeping procedures based on the methodology presented in the book "Multiple Testing Problems in Pharmaceutical Statistics" (edited by Alex Dmitrienko, Ajit C. Tamhane and Frank Bretz) published by Chapman and Hall/CRC Press 2009.

Implementation of Warnes & Raftery's MCGibbsit run-length and convergence diagnostic for a set of (not-necessarily independent) Markov Chain Monte Carlo (MCMC) samplers. It combines the quantile estimate error-bounding approach of the Raftery and Lewis MCMC run length diagnostic `gibbsit` with the between verses within chain approach of the Gelman and Rubin MCMC convergence diagnostic.

Programmatic interface to several NASA Earth Observation OPeNDAP servers (Open-source Project for a Network Data Access Protocol) (<https://www.opendap.org/>). Allows for easy downloads of MODIS subsets, as well as other Earth Observation datacubes, in a time-saving and efficient way : by sampling it at the very downloading phase (spatially, temporally and dimensionally).

This package provides methods for the analysis of how ecological drivers affect the multifunctionality of an ecosystem based on methods of Byrnes et al. 2016 <doi:10.1111/2041-210X.12143> and Byrnes et al. 2022 <doi:10.1101/2022.03.17.484802>. Most standard methods in the literature are implemented (see vignettes) in a tidy format.

This package contains a collection of functions for performing different kinds of calculation that are of interest to someone following a diet plan. Calculators for the Basal Metabolic Rate are based on Mifflin et al. (1990) <doi:10.1093/ajcn/51.2.241> and McArdle, W. D., Katch, F. I., & Katch, V. L. (2010, ISBN:9780812109917).

Simple and flexible quizzes in shiny'. Easily create quizzes from various pre-built question and choice types or create your own using htmltools and shiny packages as building blocks. Integrates with larger shiny applications. Ideal for non-web-developers such as educators, data scientists, and anyone who wants to assess responses interactively in a small form factor.

Visualization and analysis of spatially resolved transcriptomics data. The spatialGE R package provides methods for visualizing and analyzing spatially resolved transcriptomics data, such as 10X Visium, CosMx, or csv/tsv gene expression matrices. It includes tools for spatial interpolation, autocorrelation analysis, tissue domain detection, gene set enrichment, and differential expression analysis using spatial mixed models.

Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of dynamic survival models with shrinkage priors. Details on the algorithms used are provided in Wagner (2011) <doi:10.1007/s11222-009-9164-5>, Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.

Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.

Download geographic shapes from the United States Census Bureau TIGER/Line Shapefiles <https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>. Functions support downloading and reading in geographic boundary data. All downloads can be set up with a cache to avoid multiple downloads. Data is available back to 2000 for most geographies.

An interface to Zonation software, enabling users to run spatial conservation prioritization workflows in R'. It streamlines input preparation, execution, and post-processing, while supporting reproducibility and lowering the entry barrier for learning, teaching, and research in conservation planning. The methods implemented in Zonation are described in Moilanen et al. (2022) <doi:10.1111/2041-210X.13819>.

This package provides a suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

The package AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to:

• analyze germline epimutations in the context of multi-generational mutation accumulation lines;

• analyze somatic epimutations in the context of plant development and aging.

This package provides an R interface to the nanoarrow C library and the Apache Arrow application binary interface. Functions to import and export ArrowArray, ArrowSchema, and ArrowArrayStream C structures to and from R objects are provided alongside helpers to facilitate zero-copy data transfer among R bindings to libraries implementing the Arrow C data interface.

This package is a parser to import HiC data into R. It accepts several type of data: tabular files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files. The HiC data can be several files, for several replicates and conditions. The data is formated in an InteractionSet object.

MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

This package contains data required to run examples in prebs package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie).

This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.

This package provides a method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic distance. This package contains code for running analyses (which are implemented in the modeling language rstan') and visualizing and interpreting output. See the paper for more details on the model and its utility.

Quality control and formatting tools developed for the Copernicus Data Rescue Service. The package includes functions to handle the Station Exchange Format (SEF), various statistical tests for climate data at daily and sub-daily resolution, as well as functions to plot the data. For more information and documentation see <https://datarescue.climate.copernicus.eu/st_data-quality-control>.

This package provides discrete and continuous color palettes derived from the album cover artwork of each Taylor Swift Era. Each palette ships with a curated order-of-use so that smaller discrete subsets remain harmonious, and supports continuous interpolation via grDevices::colorRampPalette() for arbitrary n'. Designed to plug into ggplot2 workflows through standard manual and gradient scales.

Generates Hadamard matrices using different construction methods. For those who want to generate Hadamard matrix, a generic function, Hadamard_matrix() is provided. For those who want to generate Hadamard matrix using a particular method, separate functions are available. See Horadam (2007, ISBN:9780691119212) Hadamard Matrices and their applications, Princeton University Press for more information on Hadamard Matrices.

This package implements an estimation method for Hawkes processes when count data are only observed in discrete time, using a spectral approach derived from the Bartlett spectrum, see Cheysson and Lang (2020) <arXiv:2003.04314>. Some general use functions for Hawkes processes are also included: simulation of (in)homogeneous Hawkes process, maximum likelihood estimation, residual analysis, etc.

Includes support for Mapbox Navigation APIs, including directions, isochrones, and route optimization; the Search API for forward and reverse geocoding; the Maps API for interacting with Mapbox vector tilesets and visualizing Mapbox maps in R; and Mapbox Tiling Service and tippecanoe for generating map tiles. See <https://docs.mapbox.com/api/> for more information about the Mapbox APIs.