Packages — R (Page 3 of 7)

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-htmltable 1.11.0 — 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 0.9 — 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 1.3.5 — 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-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-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 2.3.1 — 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-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 1.18.0 — 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 1.17 — 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 1.5.1 — 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-limma 3.34.4 — 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 1.1-14 — 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 1.7.1 — 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-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 7.3-47 — 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 0.52.2 — 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-methylkit 1.4.0 — 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 1.8-22 — 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 1.4-2.1 — 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.

r-modelmetrics 1.1.0 — Rapid calculation of model metrics

Written in C++ using Rcpp, this package provides a collection of metrics for evaluating models.

r-modeltools 0.2-21 — Tools and classes for statistical models

This package provides a collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future.

r-motifrg 1.22.0 — Discover motifs in high throughput sequencing data

This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods.

r-msnbase 2.4.0 — Base functions and classes for MS-based proteomics

This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.

r-msnid 1.12.1 — Utilities for LC-MSn proteomics identifications

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

r-multitaper 1.0-14 — Multitaper spectral analysis tools

This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.

r-munsell 0.4.3 — Munsell colour system

The Munsell package contains Functions for exploring and using the Munsell colour system.

r-mutationalpatterns 1.4.1 — Extract and visualize mutational patterns in genomic data

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

r-mvtnorm 1.0-6 — Package for multivariate normal and t-distributions

This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities.

r-mzid 1.16.0 — Parser for mzIdentML files

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.

r-mzr 2.12.0 — Parser for mass spectrometry data files

The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

r-nlme 3.1-131 — Linear and nonlinear mixed effects models

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models.

r-nloptr 1.0.4 — R interface to NLopt

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

r-nmf 0.20.6 — Algorithms and framework for nonnegative matrix factorization

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

r-nnet 7.3-12 — Feed-forward neural networks and multinomial log-linear models

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

r-numderiv 2016.8-1 — Accurate numerical derivatives

This package provides methods for calculating accurate numerical first and second order derivatives.

r-openssl 0.9.9 — Toolkit for encryption, signatures and certificates

This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and bignum math methods for manually performing crypto calculations on large multibyte integers.

r-optparse 1.4.4 — Command line option parser

This package provides a command line parser inspired by Python's optparse library to be used with Rscript to write shebang scripts that accept short and long options.

r-org-ce-eg-db 3.5.0 — Genome wide annotation for Worm

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

r-org-dm-eg-db 3.5.0 — Genome wide annotation for Fly

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

r-org-hs-eg-db 3.5.0 — Genome wide annotation for Human

This package contains genome-wide annotations for Human, primarily based on mapping using Entrez Gene identifiers.

r-org-mm-eg-db 3.5.0 — Genome wide annotation for Mouse

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus.

r-organismdbi 1.20.0 — Software to enable the smooth interfacing of database packages

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

r-pbapply 1.3-3 — Adding progress bar to apply functions

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.

r-pbkrtest 0.4-7 — Methods for linear mixed model comparison

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

r-pcamethods 1.70.0 — Collection of PCA methods

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.

r-pcapp 1.9-72 — Robust PCA by projection pursuit

This package provides functions for robust principal component analysis (PCA) by projection pursuit.

r-pdist 1.2 — Partitioned distance function

Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling dist, but this creates unnecessary computation by computing the distances between a row of X and another row of X, and likewise for Y. Pdist strictly computes distances across the two matrices, not within the same matrix, making computations significantly faster for certain use cases.

r-performanceanalytics 1.4.3541 — Econometric tools for performance and risk analysis

This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

r-permute 0.9-4 — Functions for Generating Restricted Permutations of Data

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). permute also allows split-plot designs, in which the whole-plots or split-plots or both can be freely exchangeable.

r-pheatmap 1.0.8 — Pretty heatmaps

This package provides an implementation of heatmaps that offers more control over dimensions and appearance.

r-pkgconfig 2.0.1 — Private configuration for R packages

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.

r-pkgmaker 0.22 — Package development utilities

This package provides some low-level utilities to use for R package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities.

r-plogr 0.1-1 — R bindings for the plog C++ logging library

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.

r-plotly 4.7.1 — Create interactive web graphics

This package enables the translation of ggplot2 graphs to an interactive web-based version and/or the creation of custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.

r-plotrix 3.7 — Various plotting functions

This package provides lots of plotting, various labeling, axis and color scaling functions for R.

r-plyr 1.8.4 — Tools for Splitting, Applying and Combining Data

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.

r-png 0.1-7 — Read and write PNG images

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

r-powerlaw 0.70.1 — Tools for the analysis of heavy tailed distributions

This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.

r-prabclus 2.2-6 — Parametric bootstrap tests for spatial neighborhood clustering

This package provides distance-based parametric bootstrap tests for clustering with spatial neighborhood information. It implements some distance measures, clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection.

r-pracma 2.1.1 — Practical numerical math functions

This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.

r-praise 1.0.0 — Functions to praise users

This package provides template functions to assist in building friendly R packages that praise their users.