Multi-block data analysis concerns the analysis of several sets of variables (blocks) observed on the same group of individuals. The main aims of the RGCCA package are: to study the relationships between blocks and to identify subsets of variables of each block which are active in their relationships with the other blocks. This package allows to (i) run R/SGCCA and related methods, (ii) help the user to find out the optimal parameters for R/SGCCA such as regularization parameters (tau or sparsity), (iii) evaluate the stability of the RGCCA results and their significance, (iv) build predictive models from the R/SGCCA. (v) Generic print() and plot() functions apply to all these functionalities.

This package provides a comprehensive interface to the Biological Magnetic Resonance Data Bank ('BMRB') <https://bmrb.io>, mirroring all functionality of the PyBMRB Python package (v3.0). Provides four modules: (1) ChemicalShift for fetching per-entry chemical shift data from the BMRB REST API or local NMR-STAR files; (2) ChemicalShiftStatistics for database-wide statistical queries; (3) Spectra for simulating 1H-15N HSQC', 1H-13C HSQC', 1H-1H TOCSY', and generic 2D NMR spectra as interactive plots; and (4) Histogram for chemical shift distribution visualizations with optional filtering by pH, temperature, and ambiguity code. All interactive plots are rendered via plotly'. Uses the BMRB REST API v2 <https://api.bmrb.io/v2/>.

This package provides an end-to-end workflow for NASA Global Ecosystem Dynamics Investigation (GEDI) Level 1B, Level 2A, Level 2B, Level 3, Level 4A, and Level 4B data. Functions search NASA catalogues, download granules, stream HDF5 products from Earthdata Cloud, and extract geolocations, waveforms, elevation and relative-height metrics, canopy cover, plant area profiles, and aboveground biomass. Methods quality-filter and spatially clip HDF5, tabular, and raster products; calculate footprint and polygon statistics; create gridded summaries; and visualize orbital tracks and measurements. The package also simulates GEDI-like waveforms from airborne laser-scanning point clouds and supports spatial sampling, predictive modelling, ancillary-data extraction, and wall-to-wall upscaling with optional Google Earth Engine workflows.

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

The main function of this package is beep(), with the purpose to make it easy to play notification sounds on whatever platform you are on. It is intended to be useful, for example, if you are running a long analysis in the background and want to know when it is ready.

The package DAPAR is a Bioconductor distributed R package which provides all the necessary functions to analyze quantitative data from label-free proteomics experiments. Contrarily to most other similar R packages, it is endowed with rich and user-friendly graphical interfaces, so that no programming skill is required (see `Prostar` package).

The VISTA (Visualization and Integrated System for Transcriptomic Analysis) platform streamlines differential expression workflows by wrapping DESeq2 and edgeR into a SummarizedExperiment-based container with consistent metadata. The package includes visualization utilities, MSigDB enrichment helpers, and optional deconvolution support to simplify interactive exploration of RNA-seq experiments.

The functions are designed to calculate the most widely-used county-level variables in agricultural production or agricultural-climatic and weather analyses. To operate some functions in this package needs download of the bulk PRISM raster. See the examples, testing versions and more details from: <https://github.com/ysd2004/acdcR>.

This package implements inverse probability weighted, regression adjustment, and multiply robust estimators under the available complete-case missing value assumption of Cheng, Chen, Smith, and Zhao (2022) <doi:10.48550/arXiv.2207.02289>. Supports one or two primary variables, exponential-tilt sensitivity analysis, regression weights, and nonparametric bootstrap confidence intervals.

This package provides a framework and toolkit to guide R dashboard developers in implementing the Behavioral Insight Design (BID) framework. The package offers functions for documenting each of the five stages (Interpret, Notice, Anticipate, Structure, and Validate), along with a comprehensive concept dictionary. Works with both shiny applications and Quarto dashboards.

Buckley-James regression for right-censoring survival data with high-dimensional covariates. Implementations for survival data include boosting with componentwise linear least squares, componentwise smoothing splines, regression trees and MARS. Other high-dimensional tools include penalized regression for survival data. See Wang and Wang (2010) <doi:10.2202/1544-6115.1550>.

This package provides methods to perform block diagonal covariance matrix detection using singular vectors ('BD-SVD'), which can be extended to inherently sparse principal component analysis ('IS-PCA'). The methods are described in Bauer (2025) <doi:10.1080/10618600.2024.2422985> and Bauer (2026) <doi:10.48550/arXiv.2510.03729>.

Contrast analysis for factorial designs provides an alternative to the traditional ANOVA approach, offering the distinct advantage of testing targeted hypotheses. The foundation of this package is primarily rooted in the works of Rosenthal, Rosnow, and Rubin (2000, ISBN: 978-0521659802) as well as Sedlmeier and Renkewitz (2018, ISBN: 978-3868943214).

This package implements the general template for collaborative targeted maximum likelihood estimation. It also provides several commonly used C-TMLE instantiation, like the vanilla/scalable variable-selection C-TMLE (Ju et al. (2017) <doi:10.1177/0962280217729845>) and the glmnet-C-TMLE algorithm (Ju et al. (2017) <arXiv:1706.10029>).

This package provides a robust constrained L1 minimization method for estimating a large sparse inverse covariance matrix (aka precision matrix), and recovering its support for building graphical models. The computation uses linear programming. The method was published in TT Cai, W Liu, X Luo (2011) <doi:10.1198/jasa.2011.tm10155>.

Mechanistically models/predicts the phenology (macro-phases) of 10 crop plants (trained on a big dataset over 80 years derived from the German weather service (DWD) <https://opendata.dwd.de/>). Can be applied for remote sensing purposes, dynamically check the best subset of available covariates for the given dataset and crop.

The purpose of this package is to provide a comprehensive R interface to the Decision Support System for Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM; see <https://dssat.net> for more information). The package provides cross-platform functions to read and write input files, run DSSAT-CSM, and read output files.

This package provides a ggplot2 geom and position for visualizing brain region data on cortical, subcortical, and white matter tract atlases. Brain atlas geometries are stored as polygon data, enabling seamless integration with the ggplot2 ecosystem including faceting, custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020) <doi:10.1177/2515245920928009>.

This package provides tools for species distribution modeling using H3 hexagonal grids (Uber Technologies Inc., 2022, <https://h3geo.org>). Facilitates retrieval of species occurrence records, generation of H3 grids, computation of landscape metrics, and preparation of spatial data for modern species distribution models workflows. Designed for biodiversity and landscape ecology research.

Finds optimal designs for nonlinear models using a metaheuristic algorithm called Imperialist Competitive Algorithm (ICA). See, for details, Masoudi et al. (2022) <doi:10.32614/RJ-2022-043>, Masoudi et al. (2017) <doi:10.1016/j.csda.2016.06.014> and Masoudi et al. (2019) <doi:10.1080/10618600.2019.1601097>.

This package implements a computational framework to predict microbial community-based metabolic profiles with O2PLS model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.

An implementation of the iterative proportional fitting (IPFP), maximum likelihood, minimum chi-square and weighted least squares procedures for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multidimensional). The package also provides an application of the IPFP to simulate multivariate Bernoulli distributions.

This package provides functions to handle ordinal relations reflected within the feature space. Those function allow to search for ordinal relations in multi-class datasets. One can check whether proposed relations are reflected in a specific feature representation. Furthermore, it provides functions to filter, organize and further analyze those ordinal relations.

This package provides a programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), iNaturalist', eBird', Integrated Digitized Biocollections ('iDigBio'), VertNet', Ocean Biogeographic Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.