This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1.

This package contains an S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.

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 is a package for exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.

This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.

RuSTy is a IEC 61131-3 ST compiler written in Rust. It compiles ST down to native machine code, targeting most llvm-supported targets.

The empirical transition matrix (etm) package estimates the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator.

This is a package for developers to check user-supplied function arguments. It is designed to be simple, fast and customizable. Error messages follow the tidyverse style guide.

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an XPath "interpreter".

River is a dynamic tiling Wayland compositor with flexible runtime configuration. It can run nested in an X11/Wayland session or also directly from a tty using KMS/DRM.

This package provides a R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.

RDKit is a C++ and Python library for cheminformatics, which includes (among other things) the analysis and modification of molecules in 2D and 3D and descriptor generation for machine learning.

This is a package containing Public Key Infrastructure functions such as verifying certificates, RSA encryption and signing, which can be used to build PKI infrastructure and perform cryptographic tasks.

This package provides a modern module system for R. Organize code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.

This package provides a menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of Markov chain Monte Carlo (MCMC) sampling output.

This package provides alternative implementations of some base R functions, including sort, order, and match. The functions are simplified but can be faster or have other advantages.

Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, <doi:10.1093/bioinformatics/btw429>.

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

This package provides a transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

The Structural Topic Model (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions.

This package provides a cross-platform Zip compression library for R. It is a replacement for the zip function, that does not require any additional external tools on any platform.

This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time.