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 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.

This package provides a bridge is created between existing robust open-source record linkage algorithms and an urgently needed user-friendly platform that removes financial and technical barriers, setting a new standard for data interoperability in public health and bioinformatics. The fastLink algorithms are used for matching. Ted Enamorado et al. (2019) <doi:10.1017/S0003055418000783>.

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.

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>.

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.

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.

The biodbHmdb library is an extension of the biodb framework package that provides access to the HMDB Metabolites database. It allows to download the whole HMDB Metabolites database locally, access entries and search for entries by name or description. A future version of this package will also include a search by mass and mass spectra annotation.

This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections.

This package provides an interface to any collection of data sets within a single iSEE web-application. The main functionality of this package is to define a custom landing page allowing app maintainers to list a custom collection of data sets that users can selected from and directly load objects into an iSEE web-application.

This package provides a fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.

survClust is an outcome weighted integrative clustering algorithm used to classify multi-omic samples on their available time to event information. The resulting clusters are cross-validated to avoid over overfitting and output classification of samples that are molecularly distinct and clinically meaningful. It takes in binary (mutation) as well as continuous data (other omic types).

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 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 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.

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.

Dataset and functions from the meta-analysis published in Medicine & Science in Sports & Exercise. It contains all the data and functions to reproduce the analysis. "Effectiveness of HIIE versus MICT in Improving Cardiometabolic Risk Factors in Health and Disease: A Meta-analysis". Felipe Mattioni Maturana, Peter Martus, Stephan Zipfel, Andreas M Nieà (2020) <doi:10.1249/MSS.0000000000002506>.

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.

This package provides a lightweight package designed to facilitate statistical simulations through functional programming. It centralizes the simulation process into a single higher-order function, enhancing manageability and usability without adding overhead from external dependencies. The package includes ready-to-use functions for common simulation targets. A detailed example can be found on <https://github.com/ielbadisy/mcstatsim>.

This package provides a set of commands to manage an abstract optimization method. The goal is to provide a building block for a large class of specialized optimization methods. This package manages: the number of variables, the minimum and maximum bounds, the number of non linear inequality constraints, the cost function, the logging system, various termination criteria, etc...