Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

This package provides a minimal package for downloading data from GitHub repositories of the nflverse project.

Introduces optional types with some() and none, as well as match_with() from functional languages.

Simulate the dynamic of lion populations using a specific Individual-Based Model (IBM) compiled in C.

Data on the Spy vs. Spy comic strip of Mad magazine, created and written by Antonio Prohias.

Component analysis for three-way data arrays by means of Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models.

This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.

This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues, which is usually more efficient than eigen() if k << n.

raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided.

Perform wavelet analysis (orthogonal,translation invariant, tensorial, 1-2-3d transforms, thresholding, block thresholding, linear,...) with applications to data compression or denoising/regression. The core of the code is a port of MATLAB Wavelab toolbox written by D. Donoho, A. Maleki and M. Shahram (<https://statweb.stanford.edu/~wavelab/>).

Interface to use and access Wilensky's NetLogo (Wilensky 1999) from R using either headless (no GUI) or interactive GUI mode. Provides functions to load models, execute commands, and get values from reporters. Mostly analogous to the NetLogo Mathematica Link <https://github.com/NetLogo/Mathematica-Link>.

Discretize AR(1) process following Tauchen (1986) <http://www.sciencedirect.com/science/article/pii/0165176586901680>. A discrete Markov chain that approximates in the sense of weak convergence a continuous-valued univariate Autoregressive process of first order is generated. It is a popular method used in economics and in finance.

Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of ruminate is to create a shiny interface to make these tools more broadly available while creating reproducible results.

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

This package provides a solver for ompr based on the R Optimization Infrastructure ('ROI'). The package makes all solvers in ROI available to solve ompr models. Please see the ompr website <https://dirkschumacher.github.io/ompr/> and package docs for more information and examples on how to use it.

This package implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

This package provides basic routines for estimation of gene-specific transcriptional derivatives and visualization of the resulting velocity patterns.

This package provides an environment for teaching "Financial Engineering and Computational Finance" and for managing chronological and calendar objects.

This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms.

Rail is a nREPL client based on monroe with similar features, but aims to be a more complete implementation.

This package provides a unit testing system for R designed to be fun, flexible and easy to set up.

rss-bridge generates Atom feeds for social networking websites lacking feeds. Supported websites include Facebook, Twitter, Instagram and YouTube.

CBN2Path package provides a unifying interface to facilitate CBN-based quantification, analysis and visualization of cancer progression pathways.

This package provides a package to analyze flow cytometric data of complex microbial communities based on histogram images.