This small library contains a series of simple tools for constructing and manipulating confounded and fractional factorial designs.

This package provides some functions for sample classification in microarrays.

This package provides recursive partitioning functions for classification, regression and survival trees.

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

This package provides output formats and utilities for authoring books and technical documents with R Markdown.

This package extends the ggplot2 plotting system to support network visualization. Inspired by ggtree, ggtangle is designed to work with network associated data.

This package adds additional Twitter Bootstrap components to Shiny.

Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in ggplot2.

This package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.

Framework for visualising tables of counts, proportions and probabilities. The framework is called product plots, alluding to the computation of area as a product of height and width, and the statistical concept of generating a joint distribution from the product of conditional and marginal distributions. The framework, with extensions, is sufficient to encompass over 20 visualisations previously described in fields of statistical graphics and infovis, including bar charts, mosaic plots, treemaps, equal area plots and fluctuation diagrams.

This package provides functions for working with the scrypt key derivation functions. Scrypt is a password-based key derivation function created by Colin Percival. The algorithm was specifically designed to make it costly to perform large-scale custom hardware attacks by requiring large amounts of memory.

Algebraic procedures for analyses of multiple social networks are delivered with this package. multiplex makes possible, among other things, to create and manipulate multiplex, multimode, and multilevel network data with different formats. Effective ways are available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup with decomposition procedures or semiring structures with the relational bundles occurring in different types of multivariate networks. multiplex provides also an algebraic approach for affiliation networks through Galois derivations between families of the pairs of subsets in the two domains of the network with visualization options.

This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import package bridges some of the gap between using library (or require) and direct (single-object) imports. Furthermore the imported objects are not placed in the current environment. It is also possible to import objects from stand-alone .R files.

This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file. It also may be converted into other popular R objects. This package provides a link between VCF data and familiar R software.

This package provides tools to help working with text files. It can return the number of lines; print the first and last lines; convert encoding. Operations are made without reading the entire file before starting, resulting in good performances with large files.

This package provides tools for shrunken centroids regularized discriminant analysis for the purpose of classifying high dimensional data.

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. This package also supports rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.

This package provides a collection of evaluation metrics, including loss, score and utility functions, that measure regression, classification and ranking performance.

This package provides a micro-package for reading "passwords", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently, RStudio, the command line (every OS), and any platform where tcltk is present are supported.

This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

This package provides tools to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied.

Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.

This is a package to read raw accelerometry from GT3X+ accelerometry data and plain table data to calculate the Activity Index from Bai et al. (2016) doi:10.1371/journal.pone.0160644.

This package provides geometries to plot network objects with the ggplot2 package.