Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R.

Create and customize interactive maps using the Leaflet JavaScript library and the htmlwidgets package. These maps can be used directly from the R console, from RStudio, in Shiny applications and R Markdown documents.

blame outputs an annotated revision from each RCS file. An annotated RCS file describes the revision and date in which each line was added to the file, and the author of each line.

This package provides a general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019.

This package implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).

This package provides methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.

This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well as a boxplot function.

Lp_solve is software for solving linear, integer and mixed integer programs. This implementation supplies a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems.

Statistical and biological validation of clustering results. This package implements Dunn Index, Silhouette, Connectivity, Stability, BHI and BSI. Further information can be found in Brock, G et al. (2008) <doi: 10.18637/jss.v025.i04>.

RQ (Redis Queue) is a simple Python library for queueing jobs and processing them in the background with workers. It is backed by Redis and it is designed to have a low barrier to entry.

WWTD is a Travis Simulator that lets you run test matrices defined in .travis.yml on your local machine, using rvm, rbenv, or chruby to test different versions of Ruby.

The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++.

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

The affyILM package is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behal of the Langmuir model.

This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy or are discontinuous at the solution.

This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses, Rcpp, RStudio projects, and more.

This package provides tools to obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.

The rasdaemon daemon monitors platform RAS reports from Linux kernel trace events. These trace events are logged in /sys/kernel/debug/tracing and reported through standard log mechanisms like syslog.

This package provides a Ruby implementation of RFC5869: HKDF. The goal of HKDF is to take some source key material and generate suitable cryptographic keys from it.

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. Objects are implemented as R6 classes.

This package provides functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.

Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.