Pry is an IRB alternative and runtime developer console for Ruby. It features syntax highlighting, a plugin architecture, runtime invocation, and source and documentation browsing.

Ruby/Git is a Ruby library that can be used to create, read and manipulate Git repositories by wrapping system calls to the git binary.

This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.

This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

randfold computes the probability that, for a given sequence, the Minimum Free Energy (MFE) of the secondary structure is different from MFE computed with random sequences.

This package converts the output of the Sailfish and Salmon RNA-seq quantification tools so that it can be used with the Sleuth differential analysis package.

SCENIC (Single-cell regulatory network inference and clustering) is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography.

This package provides density, distribution, quantile and hazard functions of a stable variate, as well as generalized regression models for the parameters of a stable distribution.

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality.

This package implements a generalized version of principal components analysis (GLM-PCA) for dimension reduction of non-normally distributed data such as counts or binary matrices.

Camv-rnd is a viewer for PCB supporting gerber, excellon and g-code. It is part of the RiNgDove EDA suite.

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

rTorrent is a BitTorrent client with an ncurses interface. It supports full encryption, DHT, PEX, and Magnet Links. It can also be controlled via XML-RPC over SCGI.

This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.

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.

This package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.

This package lets you download Google fonts and generate CSS to use in rmarkdown documents and Shiny applications. Some popular fonts are included and ready to use.

This package provides utilities for working with Google APIs. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.

This package provides a convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. reprex also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.