This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.

This package provides a simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's faraday gem.

This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.

This package supports twin models that are able to estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.

This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

ramr is an R package for detection of epimutations (i.e., infrequent aberrant DNA methylation events) in large data sets obtained by methylation profiling using array or high-throughput methylation sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.

This package provides several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.

This package provides an R interface to the Lawson-Hanson implementation of an algorithm for non-negative least squares (NNLS). It also allows the combination of non-negative and non-positive constraints.

It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first.

This package provides functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A.C. Davison and D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

This package provides a Common Lisp library for fetching and parsing RSS feeds data via HTTP. Currently, it supports RSS versions 0.90, 0.91, and 0.92 as well as RSS version 2.

MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).

RSound allows you to send audio from an application and transfer it directly to a different computer on your LAN network. It is an audio daemon with a much different focus than most other audio daemons.

This package discovers differential features in hetero- and homogeneous omic data by a two-step method including subsampling LIMMA and NSCA. DECO reveals feature associations to hidden subclasses not exclusively related to higher deregulation levels.

This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

reproc (Redirected Process) is a C/C++ library that simplifies starting, stopping and communicating with external programs. The main use case is executing command line applications directly from C or C++ code and retrieving their output.

ICGE is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.

ACDm is a package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. It creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD models and tests them.

This package provides functions related to L-moments: computation of L-moments and trimmed L-moments of distributions and data samples; parameter estimation; L-moment ratio diagram; plot vs. quantiles of an extreme-value distribution.

The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.

This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.