FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS).

`orthosData` is the companion ExperimentData package to the `orthos` R package for mechanistic studies using differential gene expression experiments. It provides functions for retrieval from ExperimentHub and local caching of the models and datasets used internally in orthos.

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.

This package provides a collection of functions that make it easier to understand crime (or other) data, and assist others in understanding it. The package helps you read data from various sources, clean it, fix column names, and graph the data.

Description of statistical associations between variables : measures of local and global association between variables (phi, Cramér V, correlations, eta-squared, Goodman and Kruskal tau, permutation tests, etc.), multiple graphical representations of the associations between variables (using ggplot2') and weighted statistics.

Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.

This package produces SPSS- and SAS-like output for linear discriminant function analysis and canonical correlation analysis. The methods are described in Manly & Alberto (2017, ISBN:9781498728966), Rencher (2002, ISBN:0-471-41889-7), and Tabachnik & Fidell (2019, ISBN:9780134790541).

Employ time-calibrated phylogenies and trait/range data to test for differences in diversification rates over evolutionary time. Extend the STRAPP test from BAMMtools::traitDependentBAMM() to any time step along phylogenies. See inst/COPYRIGHTS for details on third-party code.

This package provides a convenient API interface to access immunological data within the CAVD DataSpace'(<https://dataspace.cavd.org>), a data sharing and discovery tool that facilitates exploration of HIV immunological data from pre-clinical and clinical HIV vaccine studies.

This package provides methods for testing the equality of dependent intraclass correlation coefficients (ICCs) estimated using linear mixed-effects models. Several of the implemented approaches are based on the work of Donner and Zou (2002) <doi:10.1111/1467-9884.00324>.

This package performs Bayesian wavelet analysis using individual non-local priors as described in Sanyal & Ferreira (2017) <DOI:10.1007/s13571-016-0129-3> and non-local prior mixtures as described in Sanyal (2025) <DOI:10.48550/arXiv.2501.18134>.

Shrinkage estimator for polygenic risk prediction (PRS) models based on summary statistics of genome-wide association (GWA) studies. Based upon the methods and original PANPRS package as found in: Chen, Chatterjee, Landi, and Shi (2020) <doi:10.1080/01621459.2020.1764849>.

This package provides functions for creating and manipulating 12-tone (i.e., dodecaphonic) musical matrices using Arnold Schoenberg's (1923) serialism technique. This package can generate random 12-tone matrices and can generate matrices using a pre-determined sequence of notes.

Generates multiple imputed datasets from a substantive model compatible fully conditional specification model for time-to-event data. Our method assumes that the censoring process also depends on the covariates with missing values. Details will be available in an upcoming publication.

This package provides a formula sub is a subformula of formula if all the terms on the right hand side of sub are terms of formula and their left hand sides are identical. This package aids in the creation of subformulas.

This package provides a wrapper for the download.file function, making it possible to download files over HTTPS across platforms. The RCurl package provides this functionality (and much more) but has external dependencies. This package has is implemented purely in R.

Recursive partitioning based on psychometric models, employing the general MOB algorithm (from package partykit) to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models.

This module provides a basic framework for creating and maintaining RDF Site Summary (RSS) files. This distribution also contains many examples that allow you to generate HTML from an RSS, convert between 0.9, 0.91, and 1.0 version, and more.

This package provides a modeling package compiling applicability domain methods in R. It combines different methods to measure the amount of extrapolation new samples can have from the training set. See <doi:10.4018/IJQSPR.2016010102> for an overview of applicability domains.

Processes survey data and displays estimation results along with the relative standard error in a table, including the number of samples and also uses a t-distribution approach to compute confidence intervals, similar to SPSS (Statistical Package for the Social Sciences) software.

The deltaPlotR package implements Angoff's Delta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality assumption or by prior determination. Item purification is supported (Magis and Facon (2014) <doi:10.18637/jss.v059.c01>).

Computational tools for meta-analysis of diagnostic accuracy test. Bootstrap-based computational methods of the confidence interval for AUC of summary ROC curve and some related AUC-based inference methods are available (Noma et al. (2021) <doi:10.1080/23737484.2021.1894408>).

This package provides a set of extensions for the ergm package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.