This package contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.

This package aims to identify candidate genes that are differentially methylated between cases and controls. It applies Student's t-test and delta beta analysis to identify candidate genes containing multiple CpG sites.

This tool provides an algorithm to identify rare cell types in single-cell data. It also identifies abundant cell types. The method is based on transcript counts obtained with unique molecular identifies.

This package includes functions for processing GeoJson objects relying on RFC 7946. The geojson encoding is based on json11, a tiny JSON library for C++11. Furthermore, the source code is exported in R through the Rcpp and RcppArmadillo packages.

This package provides a unified parallelization framework for multiple backends. This package is designed for internal package and interactive usage. The main operation is parallel mapping over lists. It supports local, multicore, mpi and BatchJobs mode. It allows tagging of the parallel operation with a level name that can be later selected by the user to switch on parallel execution for exactly this operation.

Fit Bayesian generalized (non-)linear multivariate multilevel models using Stan for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation.

This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications.

This package provides alluvial plots for ggplot2. Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables.

This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.

This package provides tools to visualize simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualizing webs, electrical networks, etc. It also includes supporting material for the book "A practical guide to ecological modelling - using R as a simulation platform" by Karline Soetaert and Peter M.J. Herman (2009) and the book "Solving Differential Equations in R" by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012).

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

This package provides datasets associated with the gap package. Currently, it includes an example data for regional association plot (CDKN), an example data for a genomewide association meta-analysis (OPG), data in studies of Parkinson's diease (PD), ALHD2 markers and alcoholism (aldh2), APOE/APOC1 markers and Schizophrenia (apoeapoc), cystic fibrosis (cf), a Olink/INF panel (inf1), Manhattan plots with (hr1420, mhtdata) and without (w4) gene annotations.

This package offers classes and functions to contact web servers while enforcing scheduling rules required by the sites. The URL class makes it easy to construct a URL by providing parameters as a vector. The Request class allows to describe Simple Object Access Protocol (SOAP) or standard requests: URL, method (POST or GET), header, body. The Scheduler class controls the request frequency for each server address by means of rules (Rule class). The RequestResult class permits to get the request status to handle error cases and the content.

This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like dplyr, tidyr and ggplot2. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.

This package provides a complete GCC cross toolchain for C/C++ development to be installed in user profiles. This includes GCC, as well as libc (headers and binariesl), and Binutils. GCC is the GNU Compiler Collection.

This package provides a complete GCC cross toolchain for C/C++ development to be installed in user profiles. This includes GCC, as well as libc (headers and binariesl), and Binutils. GCC is the GNU Compiler Collection.

This package provides a complete GCC cross toolchain for C/C++ development to be installed in user profiles. This includes GCC, as well as libc (headers and binariesl), and Binutils. GCC is the GNU Compiler Collection.

This package provides a complete GCC cross toolchain for C/C++ development to be installed in user profiles. This includes GCC, as well as libc (headers and binariesl), and Binutils. GCC is the GNU Compiler Collection.

This package provides a complete GCC cross toolchain for C/C++ development to be installed in user profiles. This includes GCC, as well as libc (headers and binariesl), and Binutils. GCC is the GNU Compiler Collection.

This package provides a cryptographic hash function that is fast, secure, parallelizable, capable of incremental updates.

Sodium is a new easy-to-use high-speed software library for network communication, encryption, decryption, signatures, etc.

Hpenc is a command-line tool for performing authenticated encryption (AES-GCM and ChaCha20-Poly1305) of streaming data. It does not perform an asymmetric key exchange, instead requiring the user to distribute pre-shared keys out of band. It is designed to handle large amounts of data quickly by using all your CPU cores and hardware acceleration.

ccrypt is a utility for encrypting and decrypting files and streams. It was designed as a replacement for the standard unix crypt utility, which is notorious for using a very weak encryption algorithm. ccrypt is based on the Rijndael block cipher, a version of which is also used in the Advanced Encryption Standard (AES, see http://www.nist.gov/aes). This cipher is believed to provide very strong security.

The Olm library implements the Double Ratchet cryptographic ratchet. It is written in C and C++11, and exposed as a C API.