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.

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.

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>.

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 provides a RESTful API wrapper for accessing the GENESIS database of the German Federal Statistical Office (Destatis) as well as its Census Database and the database of Germany's regional statistics. Supports data search functions, credential management, result caching, and handling remote background jobs for large datasets.

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/>).

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

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

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.

INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) assembled using data from public repositories.

Estimate age-depth models from stratigraphic and sedimentological data, and transform data between the time and stratigraphic domain.

This package provides functions to scrape IQY calls to Bank of Mexico, downloading and ordering the data conveniently.

This is a simple R package that allows to measure the stated preferences using traditional conjoint analysis method.

Perform a correlational class analysis of the data, resulting in a partition of the data into separate modules.