This package provides a set of functions to calculate sample size for two-sample difference in means tests. Does adjustments for either nonadherence or variability that comes from using data to estimate parameters.

This is an all-encompassing suite to facilitate the simulation of so-called quantities of interest by way of a multivariate normal distribution of the regression model's coefficients and variance-covariance matrix.

This package implements a group-bridge penalized function-on-scalar regression model proposed by Wang et al. (2023) <doi:10.1111/biom.13684>, to simultaneously estimate functional coefficient and recover the local sparsity.

This package provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) SAGA (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.

This package provides streamlined functions for summarising and visualising regression models fitted with the rms package, in the preferred format for medical journals. The modelsummary_rms() function produces concise summaries for linear, logistic, and Cox regression models, including automatic handling of models containing restricted cubic spline (RCS) terms. The resulting summary dataframe can be easily converted into publication-ready documents using the flextable and officer packages. The ggrmsMD() function creates clear and customizable plots ('ggplot2 objects) to visualise RCS terms.

This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.

This package aims to provide a pipeline for the low-level analysis of gene expression microarray data, primarily focused on the Agilent platform, but which also provides utilities which may be useful for other platforms.

This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.

This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part of the work.

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

This package provides a set of functions to run R code in an environment in which global state has been temporarily modified. Many of these functions were originally a part of the r-devtools package.

This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.

RNNoise is a noise suppression library based on a recurrent neural network. The algorithm is described in Jean-Marc Valin's paper A Hybrid DSP/Deep Learning Approach to Real-Time Full-Band Speech Enhancement.

Creating, rendering and writing BPMN diagrams <https://www.bpmn.org/>. Functionalities can be used to visualize and export BPMN diagrams created using the pm4py and bupaRminer packages. Part of the bupaR ecosystem.

This package performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.

This package implements the convex clustering through majorization-minimization (CCMM) algorithm described in Touw, Groenen, and Terada (2022) <doi:10.48550/arXiv.2211.01877> to perform minimization of the convex clustering loss function.

Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.

This package provides functions for (1) ranking, selecting, and prioritising genes, proteins, and metabolites from high dimensional biology experiments, (2) multivariate hit calling in high content screens, and (3) combining data from diverse sources.

The Discrete Transmuted Generalized Inverse Weibull (DTGIW) distribution is a new distribution for count data analysis. The DTGIW is discrete distribution based on Atchanut and Sirinapa (2021). <DOI: 10.14456/sjst-psu.2021.149>.

Functional denoising and functional ANOVA through wavelet-domain Markov groves. Fore more details see: Ma L. and Soriano J. (2018) Efficient functional ANOVA through wavelet-domain Markov groves. <arXiv:1602.03990v2 [stat.ME]>.

This package provides a network-based gene weighting algorithm for pathway enrichment analysis, using either RNA-seq or microarray data. Zhaoyuan Fang, Weidong Tian and Hongbin Ji (2012) <doi:10.1038/cr.2011.149>.

Make it easy to create simplified trial summary (TS) domain based on FDA FDA guide <https://github.com/TuCai/phuse/blob/master/inst/examples/07_genTS/www/Simplified_TS_Creation_Guide_v2.pdf>.

Analyze small-sample clustered or longitudinal data using modified generalized estimating equations with bias-adjusted covariance estimator. The package provides any combination of three modified generalized estimating equations and 11 bias-adjusted covariance estimators.