This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

This package provides an R interface to HiGHS, an optimization solver. It is designed for solving mixed-integer optimization problems with quadratic or linear objectives and linear constraints.

This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

Replication Rate (RR) is the probability of replicating a statistically significant association in genome-wide association studies. This R-package provide the estimation method for replication rate which makes use of the summary statistics from the primary study. We can use the estimated RR to determine the sample size of the replication study, and to check the consistency between the results of the primary study and those of the replication study.

The Stuttgart Neural Network Simulator (SNNS) is a library containing many standard implementations of neural networks. This package wraps the SNNS functionality to make it available from within R. Using the RSNNS low-level interface, all of the algorithmic functionality and flexibility of SNNS can be accessed. Furthermore, the package contains a convenient high-level interface, so that the most common neural network topologies and learning algorithms integrate seamlessly into R.

Datasets and utility functions to support the book "R for Plant Disease Epidemiology" (R4PDE). It includes functions for quantifying disease, assessing spatial patterns, and modeling plant disease epidemics based on weather predictors. These tools are intended for teaching and research in plant disease epidemiology. Several functions are based on classical and contemporary methods, including those discussed in Laurence V. Madden, Gareth Hughes, and Frank van den Bosch (2007) <doi:10.1094/9780890545058>.

Wraps the AT Protocol (Authenticated Transfer Protocol) behind Bluesky <https://bsky.social>. Functions can be used for, among others, retrieving posts and followers from the network or posting content.

This package implements the adaptive smoothing spline estimator for the function-on-function linear regression model described in Centofanti et al. (2023) <doi:10.1007/s00180-022-01223-6>.

This package contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.

Fits the Bayesian partial least squares regression model introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable for univariate and multivariate regression with high-dimensional data.

Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2020) <arXiv:2001.06451>.

Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.

Perform a Bayesian estimation of the exploratory deterministic input, noisy and gate (EDINA) cognitive diagnostic model described by Chen et al. (2018) <doi:10.1007/s11336-017-9579-4>.

Add a scroll back to top Font Awesome icon <https://fontawesome.com/> in rmarkdown documents and shiny apps thanks to jQuery GoTop <https://scottdorman.blog/jquery-gotop/>.

This package provides tools for multivariate nonparametrics, as location tests based on marginal ranks, spatial median and spatial signs computation, Hotelling's T-test, estimates of shape are implemented.

Mixture modelling of one-dimensional data using combinations of left-truncated Gamma, Weibull, and Lognormal Distributions. Blostein, Martin & Miljkovic, Tatjana. (2019) <doi:10.1016/j.insmatheco.2018.12.001>.

This package provides a suite of functions for reading in a rate file in XML format, stratify a cohort, and calculate SMRs from the stratified cohort and rate file.

This package provides the method for computing the local partial autocorrelation function for locally stationary wavelet time series from Killick, Knight, Nason, Eckley (2020) <doi:10.1214/20-EJS1748>.

This package provides a set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.

Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.

Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.

Large-scale gene expression studies allow gene network construction to uncover associations among genes. This package is developed for estimating and testing partial correlation graphs with prior information incorporated.

Reads in multi-part parquet files. Will read in parquet files that have not been previously coalesced into one file. Convenient for reading in moderately sized, but split files.