This package provides useful functions to edit ggplot object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends).

This package provides advanced tryCatch and try functions for better error handling (logging, stack trace with source code references and support for post-mortem analysis via dump files).

This package provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.

This package provides fast and memory efficient methods for truncated singular and eigenvalue decompositions, as well as for principal component analysis of large sparse or dense matrices.

HDF5 is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the HDF5 API using R6 classes. Additionally, functionality is added so that HDF5 objects behave very similar to their corresponding R counterparts.

This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors.

This package provides classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).

This package provides a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

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.

The package offers functions for analyzing and interactively exploring large-scale single-cell RNA-seq datasets. Pagoda2 primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. pagoda2 was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos.

This package provides an R interface to the GNU Linear Programming Kit, software for solving large-scale linear programming (LP), mixed integer linear programming (MILP) and other related problems.

This package provides fundamental physical constants (quantity, value, uncertainty, unit) for SI and non-SI units, plus unit conversions based on the data from NIST, USA.

latex2exp parses and converts LaTeX math formulas to R's plotmath expressions, used to enter mathematical formulas and symbols to be rendered as text, axis labels, etc. throughout R's plotting system.

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 the functionality to set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

This package implements heuristics for the quadratic assignment problem (QAP). Currently only a simulated annealing heuristic is available.

This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library.

This package computes moments of univariate truncated T distribution. There is only one exported function, e_trunct, which should be seen for details.

This package provides a number of methods for creating and augmenting Latin Hypercube Samples.

This package performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. It includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.

This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.

Parametric time warping aligns patterns. It aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS error and WCC. Both warping of peak profiles and of peak lists are supported.

This is a package for creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the html_pretty output format as an alternative to the html_document and html_vignette engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.

This package provides a collection of functions useful in learning and practicing Item Response Theory (IRT), which can be combined into larger programs. It provides basic CTT analysis, a simple common interface to the estimation of item parameters in IRT models for binary responses with three different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME, EAP, WLE, plausible values), item and person fit statistics, scaling methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich array of parametric and non-parametric (kernel) plots. It estimates and plots Haberman's interaction model when all items are dichotomously scored.