This package provides functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.

This package provides functions to manage taxonomy when lineages are described with strings and ranks separated with special patterns like "|*__" or ";*__".

The rocPRIM is a header-only library providing HIP parallel primitives for developing performant GPU-accelerated code on the AMD ROCm platform.

This is a package for inference of protein activity from gene expression data. It includes the VIPER and msVIPER algorithms

Real Twig is a method to correct branch overestimation in quantitative structure models. Overestimated cylinders are correctly tapered using measured twig diameters of corresponding tree species. Supported quantitative structure modeling software includes TreeQSM', SimpleForest', Treegraph', and aRchi'. Also included is a novel database of twig diameters and tools for fractal analysis of point clouds.

Download and open manifest files provided by the Copernicus Global Land Service data <https://land.copernicus.eu/global/>. The manifest files are available at: <https://land.copernicus.vgt.vito.be/manifest/>. Also see: <https://land.copernicus.eu/global/access/>. Before you can download the data, you will first need to register to create a username and password.

Reads, writes and validates mzQC files. The mzQC format is a standardized file format for the exchange, transmission, and archiving of quality metrics derived from biological mass spectrometry data, as defined by the HUPO-PSI (Human Proteome Organisation - Proteomics Standards Initiative) Quality Control working group. See <https://hupo-psi.github.io/mzQC/> for details.

This package provides simplified methods for managing classic Rubik's cubes and many other modifications of it (such as NxNxN size cubes, void cubes and 8-coloured cubes - so called octa cubes). Includes functions of handling special syntax for managing such cubes; and different approach to plotting 3D cubes without using external libraries (for example OpenGL').

Cross validate large genetic data while specifying clinical variables that should always be in the model using the function cv(). An ROC plot from the cross validation data with AUC can be obtained using rocplot(), which also can be used to compare different models. Framework was built to handle genetic data, but works for any data.

The Rearrangement Correlation Coefficient is an adjusted version of Pearson's correlation coefficient that accurately measures monotonic dependence relationships, including both linear and nonlinear associations. This method addresses the underestimation problem of classical correlation coefficients in nonlinear monotonic scenarios through improved statistical bounds derived from rearrangement inequalities. For more details, see Ai (2024) <doi:10.52202/079017-1180>.

This package provides a comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.

Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with C++ across a set of tumor samples and allows for multi-threading to decrease computational runtime.

The RSP markup language provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. Today's date is <%=Sys.Date()%>. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. RSP is ideal for self-contained scientific reports and R package vignettes.

This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Estimate generalized additive mixed models via a version of function gamm from the mgcv package, using the lme4 packagefor estimation.

This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

This package performs search for the global minimum of a very complex non-linear objective function with a very large number of optima.

Routino is an application for finding a route between two points using the dataset of topographical information collected by https://www.OpenStreetMap.org.

Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells.

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.

Coerce R object to asciidoc', txt2tags', restructuredText', org', textile or pandoc syntax. Package comes with a set of drivers for Sweave'.

Bayesian analysis for exponential random graph models using advanced computational algorithms. More information can be found at: <https://acaimo.github.io/Bergm/>.

This package provides functions to run the CRM and TITE-CRM in phase I trials and calibration tools for trial planning purposes.

Statistics and graphics for streamflow history, water quality trends, and the statistical modeling algorithm: Weighted Regressions on Time, Discharge, and Season (WRTDS).