Packages — R (Page 3 of 9)

r-ggthemes 3.4.0 — Extra themes, scales and geoms for ggplot2

This package provides extra themes and scales for ggplot2 that replicate the look of plots by Edward Tufte and Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The Wall Street Journal, among others. This package also provides geoms for Tufte's box plot and range frame.

r-git2r 0.21.0 — Access Git repositories with R

This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods.

r-gkmsvm 0.79.0 — Gapped-kmer support vector machine

This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.

r-glmnet 2.0-13 — Lasso and elastic-net regularized generalized linear models

The glmnet package provides efficient procedures for fitting the entire lasso or elastic-net regularization path for linear and Poisson regression, as well as logistic, multinomial, Cox, multiple-response Gaussian and grouped multinomial models. The algorithm uses cyclical coordinate descent in a path-wise fashion.

r-globaloptions 0.0.12 — Generate functions to get or set global options

This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.

r-glue 1.2.0 — Interpreted string literals

This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.

r-go-db 3.5.0 — Annotation maps describing the entire Gene Ontology

The purpose of this GO.db annotation package is to provide detailed information about the latest version of the Gene Ontologies.

r-googlesheets 0.2.2 — Manage Google spreadsheets from R

This package provides tools to interact with Google Sheets from within R.

r-gostats 2.44.0 — Tools for manipulating GO and microarrays

This package provides a set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

r-gower 0.1.2 — Gower's distance

This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.

r-gplots 3.0.1 — Various R programming tools for plotting data

This package provides various R programming tools for plotting data, including:

  • calculating and plotting locally smoothed summary function

  • enhanced versions of standard plots

  • manipulating colors

  • calculating and plotting two-dimensional data summaries

  • enhanced regression diagnostic plots

  • formula-enabled interface to stats::lowess function

  • displaying textual data in plots

  • baloon plots

  • plotting "Venn" diagrams

  • displaying Open-Office style plots

  • plotting multiple data on same region, with separate axes

  • plotting means and confidence intervals

  • spacing points in an x-y plot so they don't overlap

r-gprofiler 0.6.4 — Interface to the g:Profiler toolkit

This package provides tools for functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the g:Profiler toolkit.

r-gqtlbase 1.10.0 — Infrastructure for eQTL, mQTL and similar studies

The purpose of this package is to simplify the storage and interrogation of quantitative trait loci (QTL) archives, such as eQTL, mQTL, dsQTL, and more.

r-gqtlstats 1.10.1 — Computationally efficient analysis for eQTL and allied studies

This package provides tools for the computationally efficient analysis of quantitative trait loci (QTL) data, including eQTL, mQTL, dsQTL, etc. The software in this package aims to support refinements and functional interpretation of members of a collection of association statistics on a family of feature/genome hypotheses.

r-graph 1.56.0 — Handle graph data structures in R

This package implements some simple graph handling capabilities for R.

r-gridbase 0.4-7 — Integration of base and grid graphics

This package provides an integration of base and grid graphics for R.

r-gridextra 2.3 — Miscellaneous functions for "Grid" graphics

This package provides a number of user-level functions to work with grid graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

r-grohmm 1.12.0 — GRO-seq analysis pipeline

This package provides a pipeline for the analysis of GRO-seq data.

r-gseabase 1.40.1 — Gene set enrichment data structures and methods

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

r-gsubfn 0.6-6 — Utilities for strings and function arguments.

This package provides gsubfn which is like gsub but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the replacement function and replaced by the function output. gsubfn can be used to split strings based on content rather than delimiters and for quasi-perl-style string interpolation. The package also has facilities for translating formulas to functions and allowing such formulas in function calls instead of functions.

r-gtable 0.2.0 — R library to arrange grobs in tables

Gtable is a collection of tools to make it easier to work with "tables" of grobs.

r-gtools 3.5.0 — Various R programming tools

This package contains a collection of various functions to assist in R programming, such as tools to assist in developing, updating, and maintaining R and R packages, calculating the logit and inverse logit transformations, tests for whether a value is missing, empty or contains only NA and NULL values, and many more.

r-gviz 1.22.3 — Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

r-gwascat 2.10.0 — Tools for data in the EMBL-EBI GWAS catalog

This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog.

r-hardyweinberg 1.5.9 — Statistical tests and graphics for Hardy-Weinberg equilibrium

This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.

r-haven 1.1.1 — Import and Export 'SPSS', 'Stata' and 'SAS' Files

This package lets you mport foreign statistical formats into R via the embedded ReadStat C library.

r-hdf5array 1.6.0 — HDF5 back end for DelayedArray objects

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

r-heatmaply 0.14.1 — Interactive cluster heat maps using plotly

This package enables you to create interactive cluster heatmaps that can be saved as a stand-alone HTML file, embedded in R Markdown documents or in a Shiny app, and made available in the RStudio viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A heatmap is a popular graphical method for visualizing high-dimensional data, in which a table of numbers is encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by dendrograms.

r-hexbin 1.27.2 — Hexagonal binning routines

This package provides binning and plotting functions for hexagonal bins. It uses and relies on grid graphics and formal (S4) classes and methods.

r-highr 0.6 — Syntax highlighting for R source code

This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

r-hitc 1.22.0 — High throughput chromosome conformation capture analysis

The HiTC package was developed to explore high-throughput "C" data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

r-hmisc 4.1-1 — Miscellaneous data analysis and graphics functions

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.

r-hms 0.4.1 — Pretty time of day

This package implements an S3 class for storing and formatting time-of-day values, based on the difftime class.

r-homo-sapiens 1.3.1 — Annotation package for the Homo.sapiens object

This package contains the Homo.sapiens object to access data from several related annotation packages.

r-hpar 1.20.0 — Human Protein Atlas in R

This package provides a simple interface to and data from the Human Protein Atlas project.

r-htmltable 1.11.2 — Advanced tables for Markdown/HTML

This package provides functions to build tables with advanced layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying CSS-structure is simple in order to maximize compatibility with word processors such as LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML or LaTeX.

r-htmltools 0.3.6 — R tools for HTML

This package provides tools for HTML generation and output in R.

r-htmlwidgets 1.0 — HTML Widgets for R

HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.

r-httpuv 1.3.6.2 — HTTP and WebSocket server library for R

The httpuv package provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone.

r-httr 1.3.1 — Tools for working with URLs and HTTP

The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components.

r-hwriter 1.3.2 — Output R objects in HTML format

This package provides easy-to-use and versatile functions to output R objects in HTML format.

r-ica 1.0-1 — Independent component analysis

This package provides tools for Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE).

r-idr 1.2 — Irreproducible discovery rate

This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel

r-ifultools 2.0-4 — Insightful research tools

This package provides C code used by the wmtsa, fractal, and sapa R packages.

r-igraph 1.1.2 — Network analysis and visualization

This package provides routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

r-import 1.1.0 — Import mechanism for R

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.

r-impute 1.52.0 — Imputation for microarray data

This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging.

r-inline 0.3.14 — Functions to inline C, C++, Fortran function calls from R

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.

r-interactivedisplaybase 1.16.0 — Base package for web displays of Bioconductor objects

This package contains the basic methods needed to generate interactive Shiny-based display methods for Bioconductor objects.

r-ipred 0.9-6 — Improved predictors

This package provides improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

r-iranges 2.12.0 — Infrastructure for manipulating intervals on sequences

This package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

r-irlba 2.3.2 — Methods for eigendecomposition of large matrices

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.

r-iterators 1.0.9 — Iterator construct for R

This package provides support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.

r-jpeg 0.1-8 — Read and write JPEG images with R

This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors.

r-jsonlite 1.5 — Robust, high performance JSON parser and generator for R

The jsonlite package provides a fast JSON parser and generator optimized for statistical data and the web. It offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. In addition to converting JSON data from/to R objects, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

r-keggrest 1.18.1 — Client-side REST access to KEGG

This package provides a package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST server.

r-kernlab 0.9-25 — Kernel-based machine learning tools

This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods kernlab includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.

r-kernsmooth 2.23-15 — Functions for kernel smoothing

This package provides functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".

r-knitr 1.20 — General-purpose package for dynamic report generation in R

This package provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

r-knitrbootstrap 1.0.1 — Knitr bootstrap framework

This package provides a framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.

r-ksamples 1.2-7 — K-Sample rank tests and their combinations

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.

r-labeling 0.3 — Axis labeling algorithms

The labeling package provides a range of axis labeling algorithms.

r-laeken 0.4.6 — Estimation of indicators on social exclusion and poverty

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.

r-lambda-r 1.2 — Functional programming extension for R

This package provides a language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

r-lars 1.2 — Least angle regression software

Least Angle Regression ("LAR") is a model selection algorithm; a useful and less greedy version of traditional forward selection methods. A simple modification of the LAR algorithm implements Tibshirani's Lasso; the Lasso modification of LARS calculates the entire Lasso path of coefficients for a given problem at the cost of a single least squares fit. Another LARS modification efficiently implements epsilon Forward Stagewise linear regression.

r-lattice 0.20-35 — High-level data visualization system

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.

r-latticeextra 0.6-28 — Extra graphical utilities based on lattice

Building on the infrastructure provided by the lattice package, this package provides several new high-level graphics functions and methods, as well as additional utilities such as panel and axis annotation functions.

r-lava 1.6 — Latent variable models

This package provides tools for the estimation and simulation of latent variable models.

r-lazyeval 0.2.1 — Lazy (non-standard) evaluation in R

This package provides the tools necessary to do non-standard evaluation (NSE) in R.

r-ldblock 1.8.0 — Data structures for linkage disequilibrium measures in populations

This package defines data structures for linkage disequilibrium (LD) measures in populations. Its purpose is to simplify handling of existing population-level data for the purpose of flexibly defining LD blocks.

r-leaps 3.0 — Regression subset selection

This package provides tools for regression subset selection, including exhaustive search.

r-limma 3.34.9 — Package for linear models for microarray and RNA-seq data

This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.

r-limsolve 1.5.5.3 — Solving linear inverse models

This package provides functions that:

  1. find the minimum/maximum of a linear or quadratic function,

  2. sample an underdetermined or overdetermined system,

  3. solve a linear system Ax=B for the unknown x.

It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.

r-lme4 1.1-16 — Linear mixed-effects models using eigen and S4

This package provides fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen glue.

r-lmoments 1.2-3 — L-moments and quantile mixtures

This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.

r-lmtest 0.9-35 — Testing linear regression models

This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.

r-locfit 1.5-9.1 — Local regression, likelihood and density estimation

This package provides functions used for local regression, likelihood and density estimation.

r-lpsolve 5.6.13 — R interface to Lp_solve to solve linear/integer programs

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.

r-lubridate 1.7.3 — Make dealing with dates a little easier

This package provides functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

r-magrittr 1.5 — A forward-pipe operator for R

Magrittr provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."

r-maldiquant 1.17 — Quantitative analysis of mass spectrometry data

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.

r-mapproj 1.2-5 — Map projection in R

This package converts latitude/longitude into projected coordinates.

r-maps 3.2.0 — Draw geographical maps

This package provies an R module for display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

r-markdown 0.8 — Markdown rendering for R

This package provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.

r-mass 7.3-49 — Support functions and datasets for Venables and Ripley's MASS

This package provides functions and datasets for the book "Modern Applied Statistics with S" (4th edition, 2002) by Venables and Ripley.

r-matrix 1.2-12 — Sparse and dense matrix classes and methods

This package provides classes and methods for dense and sparse matrices and operations on them using LAPACK and SuiteSparse.

r-matrixmodels 0.4-1 — Modelling with sparse and dense matrices

This package models with sparse and dense matrix matrices, using modular prediction and response module classes.

r-matrixstats 0.53.1 — Methods applying to vectors and matrix rows and columns

This package provides methods operating on rows and columns of matrices, e.g. rowMedians(), rowRanks(), and rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.

r-mclust 5.4 — Gaussian mixture modelling for model-based clustering etc.

This package provides Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.

r-memoise 1.1.0 — Memoise functions for R

This R package allows to cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.

r-metap 0.8 — Meta-analysis of significance values

The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.

r-methylkit 1.4.1 — DNA methylation analysis from high-throughput bisulfite sequencing results

MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from Reduced representation bisulfite sequencing (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.

r-mgcv 1.8-23 — Mixed generalised additive model computation

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

r-mice 2.46.0 — Multivariate imputation by chained equations

Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in http://doi.org/10.18637/jss.v045.i03. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

r-microbenchmark 1.4-4 — Accurate timing functions for R

This package provides infrastructure to accurately measure and compare the execution time of R expressions.

r-mime 0.5 — R package to map filenames to MIME types

This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

r-minimal 3.4.3 — Environment for statistical computing and graphics

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.

r-minqa 1.2.4 — Derivative-free optimization algorithms by quadratic approximation

This package provides a derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

r-mixtools 1.1.0 — Tools for analyzing finite mixture models

This package provides a collection of R functions for analyzing finite mixture models.

r-mnormt 1.5-5 — Multivariate normal and "t" distributions

This package provides functions for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods.