The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

This package provides tools to create interactive chords diagrams via the D3 Javascript library. Chord diagrams show directed relationships among a group of entities. This package is based on http://bl.ocks.org/mbostock/4062006 with some modifications (fading) and additions (tooltips, bipartite diagram type).

This package contains the function ggsurvplot() for easily drawing beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot adjusted curves for Cox model and to visually examine Cox model assumptions.

Use Monte-Carlo and K-fold cross-validation coupled with machine- learning classification algorithms to perform population assignment, with functionalities of evaluating discriminatory power of independent training samples, identifying informative loci, reducing data dimensionality for genomic data, integrating genetic and non-genetic data, and visualizing results.

You can use this package to create custom pipeline badges in a standard svg format. This is useful for a company to use internally, where it may not be possible to create badges through external providers. This project was inspired by the anybadge library in python.

Use the Amazon Alexa Web Information Services API to find information about domains, including the kind of content that they carry, how popular are they---rank and traffic history, sites linking to them, among other things. See <https://aws.amazon.com/awis/> for more information.

Simulating synthetic clumped isotope dataset, fitting linear regression models under Bayesian and non-Bayesian frameworks, and generating temperature reconstructions for the same two approaches. Please note that models implemented in this package are described in Roman-Palacios et al. (2021) <doi:10.1002/essoar.10507995.1>.

Statistical summary of STRUCTURE output. STRUCTURE is a K-means clustering method for inferring population structure and assigning individuals to populations using genetic data. Pritchard JK, Stephens M, Donnelly PJ (2000) <DOI:10.1093/genetics/155.2.945>. <https://web.stanford.edu/group/pritchardlab/structure.html>.

This package provides a Bayesian method for Phenome-wide association studies (PheWAS) that identifies causal associations between genetic variants and traits, while simultaneously addressing confounding due to linkage disequilibrium. For details see Manipur et al (2024, Nature Communications) <doi:10.1038/s41467-024-49990-8>.

Based on random forest principle, DynForest is able to include multiple longitudinal predictors to provide individual predictions. Longitudinal predictors are modeled through the random forest. The methodology is fully described for a survival outcome in: Devaux, Helmer, Genuer & Proust-Lima (2023) <doi: 10.1177/09622802231206477>.

To help you access, transform, analyze, and visualize ForestGEO data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to plot ForestGEO data. To learn more about ForestGEO visit <https://forestgeo.si.edu/>.

Computes Gromov-Hausdorff type l^p distances for labeled metric spaces. These distances were introduced in V.Liebscher, Gromov meets Phylogenetics - new Animals for the Zoo of Metrics on Tree Space <arXiv:1504.05795> for phylogenetic trees, but may apply to a diversity of scenarios.

This package creates bar plots with rounded corners using ggplot2'. The code in this package was adapted from a solution provided by Stack Overflow user sthoch in the following post <https://stackoverflow.com/questions/62176038/r-ggplot2-bar-chart-with-round-corners-on-top-of-bar>.

When comparing discrete data mini bubble plots allow displaying more information than traditional bubble plots via colour, shape or labels. Exact overlapping coordinates will be transformed so they surround the original point circularly without overlapping. This is implemented as a position_surround() function for ggplot2'.

Interact with Google's Cloud Natural Language API <https://cloud.google.com/natural-language/> (v1) via R. The API has four main features, all of which are available through this R package: syntax analysis and part-of-speech tagging, entity analysis, sentiment analysis, and language identification.

Discriminant analysis and data clustering methods for high dimensional data, based on the assumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model.

This package implements the item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.

This package provides an easy way to create interactive KPI (key performance indicator) widgets for Quarto dashboards using Crosstalk'. The package enables visualization of key metrics in a structured format, supporting interactive filtering and linking with other Crosstalk'-enabled components. Designed for use in Quarto Dashboards.

This package provides tools for creating and issuing nicely-formatted text within R diagnostic messages and those messages given during warnings and errors. The formatting of the messages can be customized using templating features. Issues with singular and plural forms can be handled through specialized syntax.

Various methods for multivariate outlier detection: arw, a Mahalanobis-type method with an adaptive outlier cutoff value; locout, a method incorporating local neighborhood; pcout, a method for high-dimensional data; mvoutlier.CoDa, a method for compositional data. References are provided in the corresponding help files.

This package provides tools to generate Necklaces, Bracelets, Lyndon words and de Bruijn sequences. The generation relies on integer partitions and uses the KStatistics package. Methods used in the package refers to E. Di Nardo and G. Guarino (2022) <doi:10.48550/arXiv.2208.06855>.

This package provides a comprehensive system for designing and implementing on-farm precision field agronomic trials. You provide field data, tell ofpetrial how to design a trial, and get readily-usable trial design files and a report checks the validity and reliability of the trial design.

Simulating particle movement in 2D space has many application. The particles package implements a particle simulator based on the ideas behind the d3-force JavaScript library. particles implements all forces defined in d3-force as well as others such as vector fields, traps, and attractors.