This package provides a shiny design of experiments (DOE) app that aids in the creation of traditional, un-replicated, augmented and partially-replicated designs applied to agriculture, plant breeding, forestry, animal and biological sciences.

An interactive document on the topic of goodness of fit analysis using rmarkdown and shiny packages. Runtime examples are provided in the package function as well as at <https://predanalyticssessions1.shinyapps.io/ChiSquareGOF/>.

Analyze small-sample clustered or longitudinal data with binary outcome using modified generalized estimating equations (GEE) with bias-adjusted covariance estimator. The package provides any combination of three GEE methods and 12 covariance estimators.

Variable selection for ultrahigh-dimensional ("large p small n") linear Gaussian models using a fiducial framework allowing to draw inference on the parameters. Reference: Lai, Hannig & Lee (2015) <doi:10.1080/01621459.2014.931237>.

Some useful functions that can use grid and ggplot2 to plot sectors and interact with Seurat to plot gene expression percentages. Also, there are some examples of how to draw sectors in ComplexHeatmap'.

Enhances the H2O platform by providing tools for detailed evaluation of machine learning models. It includes functions for bootstrapped performance evaluation, extended F-score calculations, and various other metrics, aimed at improving model assessment.

Estimate the proportions of the null and the reproducibility and non-reproducibility of the signal group for the input data set. The Bayes factor calculation and EM (Expectation Maximization) algorithm procedures are also included.

This package provides a static library for Imath (see <https://github.com/AcademySoftwareFoundation/Imath>), a library for functions and data types common in computer graphics applications, including a 16-bit floating-point type.

Fits Semiparametric Promotion Time Cure Models, taking into account (using a corrected score approach or the SIMEX algorithm) or not the measurement error in the covariates, using a backfitting approach to maximize the likelihood.

This package provides functions for simulating, estimating and forecasting stationary Vector Autoregressive (VAR) models for multiple subject data using the penalized multi-VAR framework in Fisher, Kim and Pipiras (2020) <arXiv:2007.05052>.

This package provides a Shiny application to estimate the sample size required for a metabolomic experiment to achieve a desired statistical power. Estimation is possible with or without available data from a pilot study.

Test for independence of two random vectors, learn and report the dependency structure. For more information, see Gorsky, Shai and Li Ma, Multiscale Fisher's Independence Test for Multivariate Dependence, Biometrika, accepted, January 2022.

Construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis as described in Szabo, A. and Boucher, K (2002) <doi:10.1016/S0025-5564(02)00086-X>.

This extension of the poems pattern-oriented modeling (POM) framework provides a collection of modules and functions customized for paleontological time-scales, and optimized for single-generation transitions and large populations, across multiple generations.

Given a bulk transcriptomic (RNA-seq) sample of an Myeloid Leukemia patient calculates immune composition and drug resistance for different small-molecule inhibitors. Published in <https://www.nature.com/articles/s41698-024-00596-9>.

Performing Item Response Theory analysis such as parameter estimation, ability estimation, item and model fit analyse, local independence assumption, dimensionality assumption, characteristic and information curves under various models with a user friendly shiny interface.

This package provides a toolkit for working with TOML files in R while preserving formatting, comments, and structure. tomledit enables serialization of R objects such as lists, data.frames, numeric, logical, and date vectors.

Interface to the API for TreeBASE <http://treebase.org> from R. TreeBASE is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.

This package provides several analysis-related functions for the book entitled "R statistics and graph for medical articles" (written in Korean), version 1, by Keon-Woong Moon with Korean demographic data with several plot functions.

Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy interfaces to manipulate tree data.

This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.