This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan.

This package provides font files that can be used by the showtext package.

This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...

This package provides support for the foreach looping construct. foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

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 is a package for the analysis of music and speech. Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read MP3, read MIDI, perform steps of a transcription, ...

This package provides three functions for dealing with dates: parse_iso_8601 recognizes and parses all valid ISO 8601 date and time formats, parse_date parses dates in unspecified formats, and format_iso_8601 formats a date in ISO 8601 format.

This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4 byte real values). Access to parts of the matrix is done by indexing, exactly as with usual R matrices. It supports very large matrices; the package has been tested on multi-terabyte matrices. It allows for more than 2^32 rows or columns, ad allows for quick addition of extra columns to a filematrix.

This package provides interactive, configurable and graphics visualization of the chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

This package provides functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.

This package performs score test using saddlepoint approximation to estimate the null distribution. It also prepares summary statistics for meta-analysis and performs meta-analysis to combine multiple association results.

Testing and documenting code that communicates with remote servers can be painful. Dealing with authentication, server state, and other complications can make testing seem too costly to bother with. But it doesn't need to be that hard. This package enables one to test all of the logic on the R sides of the API in your package without requiring access to the remote service. Importantly, it provides three contexts that mock the network connection in different ways, as well as testing functions to assert that HTTP requests were---or were not---made. It also allows one to safely record real API responses to use as test fixtures. The ability to save responses and load them offline also enables one to write vignettes and other dynamic documents that can be distributed without access to a live server.

This package provides a framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.

This package provides a unified pipeline to clean, prepare, plot, and run basic analyses on pupillometry experiments.

Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions provided by this package splits such data into separate cells. This package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.

This package performs optimization in R using C++. A unified wrapper interface is provided to call C functions of the five optimization algorithms (Nelder-Mead, BFGS, CG, L-BFGS-B and SANN) underlying optim().

This package runs a minimum-hypergeometric (mHG) test as described in "Discovering Motifs in Ranked Lists of DNA Sequences" by Eran Eden.

OOMPA offers R packages for gene expression and proteomics analysis. OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface. All higher level analysis tools in OOMPA are compatible with the eSet classes defined in BioConductor. The lower level processing tools offer an alternative to parts of BioConductor, but can also be used to enhance existing BioConductor packages.

This package provides color palettes. They are checked for colorblind accessibility from hue, saturation, and lightness value scaling using the Chroma.js Color Palette Helper. See https://gka.github.io/palettes.

Create interactive 3D scatter plots, network plots, and globes in R using the three.js visualization library.

This package provides a Shiny app that can disconnect for a variety of reasons: an unrecoverable error occurred in the app, the server went down, the user lost internet connection, or any other reason that might cause the Shiny app to lose connection to its server. With shinydisconnect, you can call disonnectMessage anywhere in a Shiny app's UI to add a nice message when this happens. It works locally (running Shiny apps within RStudio) and on Shiny servers.

This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like standardization or bootstrapping of parameters and models, feature reduction (feature extraction and variable selection) as well as conversion between indices of effect size.

This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library.