This package provides an implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).

Designed for simplicity, a mirai evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on nanonext and NNG (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.

This package provides a re-implementation of the gWidgets API. The API is defined in this package. A second, toolkit-specific package is required to use it.

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

This is a package for slanted matrices and ordered clustering for better visualization of similarity data.

This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods.

svglite is a graphics device that produces clean SVG (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in svg(), svglite is considerably faster, produces smaller files, and leaves text as is.

This package provides a suite of elliptic and related functions including Weierstrass and Jacobi forms. It also includes various tools for manipulating and visualizing complex functions.

This package provides a comprehensive library for date-time manipulations using a new family of orthogonal date-time classes (durations, time points, zoned-times, and calendars) that partition responsibilities so that the complexities of time zones are only considered when they are really needed. Capabilities include: date-time parsing, formatting, arithmetic, extraction and updating of components, and rounding.

The fstlib library provides multithreaded serialization of compressed data frames using the fst format. The fst format allows for random access of stored data and compression with the LZ4 and ZSTD compressors.

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.

This package reads and writes data files like CSV, TSV and FWF. When reading it uses a quick initial indexing step, then reads the values lazily, so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

This package provides a shared resource interface for the bigmemory and synchronicity packages.

This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.

This package provides a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.

This package provides the Open Source Geometry Engine (GEOS) as a C API that can be used to write high-performance C and C++ geometry operations using R as an interface. Headers are provided to make linking to and using these functions from C++ code as easy and as safe as possible. This package contains an internal copy of the GEOS library to guarantee the best possible consistency on multiple platforms.

This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions.

The r-phylogram package is a tool for for developing phylogenetic trees as deeply-nested lists known as "dendrogram" objects. It provides functions for conversion between "dendrogram" and "phylo" class objects, as well as several tools for command-line tree manipulation and import/export via Newick parenthetic text. This improves accessibility to the comprehensive range of object-specific analytical and tree-visualization functions found across a wide array of bioinformatic R packages.

This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.

LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.

This package lets you create a web app that makes it easier to test web clients without using the internet. It includes a web app framework with path matching, parameters and templates. It can parse various HTTP request bodies. It can send JSON data or files from the disk. It includes a web app that implements the httpbin.org web service.

This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.