Packages — R (Page 4 of 11)

r-googlesheets 0.3.0 — Manage Google spreadsheets from R

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

r-goplot 1.0.2 — Visualization of functional analysis data

This package provides an implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its plotting functions have been developed with an hierarchical structure in mind: starting from a general overview to identify the most enriched categories (modified bar plot, bubble plot) to a more detailed one displaying different types of relevant information for the molecules in a given set of categories (circle plot, chord plot, cluster plot, Venn diagram, heatmap).

r-goseq 1.34.0 — Gene Ontology analyser for RNA-seq and other length biased data

This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

r-gostats 2.48.0 — 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 0.6.7 — 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 1.14.0 — 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 1.14.0 — 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 1.60.0 — 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 1.16.0 — GRO-seq analysis pipeline

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

r-gseabase 1.44.0 — Gene set enrichment data structures and methods

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

r-gsubfn 0.7 — 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 3.8.1 — 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 1.26.0 — 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 2.14.0 — 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-h5 0.9.9 — Interface to the HDF5 Library

This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The HDF5 format can therefore be used as an alternative to R's save/load mechanism. Since h5 is able to access only subsets of stored data it can also handle data sets which do not fit into memory.

r-hardyweinberg 1.6.1 — 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-hash 2.2.6 — Implementation of hash/associated arrays/dictionaries

This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native named lists and vectors.

r-haven 1.1.2 — 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 1.10.0 — 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-hdf5r 1.0.1 — Interface to the HDF5 binary data format

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.

r-heatmaply 0.15.2 — 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 0.7 — 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 1.26.0 — 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 0.4.2 — 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 1.24.0 — Human Protein Atlas in R

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

r-htmltable 1.12 — 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 1.3 — 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 1.4.5 — 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 1.0-2 — 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 1.2.2 — 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 1.56.0 — Imputation for microarray data

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

r-infotheo 1.2.0 — Information-theoretic measures

This package implements various measures of information theory based on several entropy estimators.

r-ini 0.3.1 — Read and write configuration files

This package provides tools to parse simple .ini configuration files to an structured list. Users can manipulate this resulting list with lapply() functions. This same structured list can be used to write back to file after modifications.

r-inline 0.3.15 — 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-inspect 1.12.0 — Analysis of 4sU-seq and RNA-seq time-course data

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.

r-interactionset 1.10.0 — Base classes for storing genomic interaction data

This packages provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

r-interactivedisplaybase 1.20.0 — 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 0.9-8 — 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 2.16.0 — 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 1.0.10 — 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-itertools 0.1-3 — Iterator tools

This package provides various tools for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the snow package.

r-jomo 2.6-5 — Multilevel Joint Modelling Multiple Imputation

Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation http://doi.org/10.1002/9781119942283. Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.

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 1.22.0 — 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 0.9-27 — 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 1.0.2 — Knitr bootstrap framework

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

r-ks 1.11.3 — Kernel smoothing

This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing.

r-ksamples 1.2-8 — 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 1.2.3 — 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-later 0.7.5 — Utilities for delaying function execution

This package provides tools to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied.

r-lattice 0.20-38 — 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 1.6.3 — 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 1.12.0 — 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-learnr 0.9.2.1 — Interactive tutorials for R

This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.

r-limma 3.38.2 — 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 1.1-19 — 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-lmertest 3.0-1 — Tests in linear mixed effects models

This package provides p-values in type I, II or III anova and summary tables for lmer model fits via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via the pbkrtest package. Model selection methods include step, drop1 and anova-like tables for random effects (ranova). Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed effects are also available.

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 0.9-36 — 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-loomr 0.2.0-1.df0144b — R interface for loom files

This package provides an R interface to access, create, and modify loom files. loomR aims to be completely compatible with loompy.

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-lsei 1.2-0 — Solve regression problems under equality/inequality constraints

It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first.

r-lubridate 1.7.4 — 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-magic 1.5-9 — Create and investigate magic squares

This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays.

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 1.18 — 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-manipulatewidget 0.10.0 — Add even more interactivity to interactive charts

This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.

r-mapproj 1.2.6 — Map projection in R

This package converts latitude/longitude into projected coordinates.

r-maps 3.3.0 — 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-maptools 0.9-4 — Tools for reading and handling spatial objects

This package provides a set of tools for manipulating and reading geographic data, in particular ESRI Shapefiles. It includes binary access to GSHHG shoreline files. The package also provides interface wrappers for exchanging spatial objects with other R packages.

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-marray 1.60.0 — Exploratory analysis for two-color spotted microarray data

This package contains class definitions for two-color spotted microarray data. It also includes fuctions for data input, diagnostic plots, normalization and quality checking.

r-mass 7.3-51.1 — 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 1.2-15 — 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.