Packages — R (Page 3 of 9)
r-genomationdata 1.10.0 — Experimental data for use with the genomation package
This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.
r-genomeinfodb 1.16.0 — Utilities for manipulating chromosome identifiers
This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
r-genomeinfodbdata 0.99.1 — Species and taxonomy ID look up tables for GenomeInfoDb
This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.
r-genomicalignments 1.16.0 — Representation and manipulation of short genomic alignments
This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.
r-genomicfeatures 1.32.0 — Tools for working with transcript centric annotations
This package provides a set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.
r-genomicfiles 1.16.0 — Distributed computing by file or by range
This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.
r-genomicinteractions 1.14.0 — R package for handling genomic interaction data
This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics.
r-genomicranges 1.32.3 — Representation and manipulation of genomic intervals
This package provides tools to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.
r-geometry 0.3-6 — Mesh generation and surface tesselation
This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.
r-geosphere 1.5-7 — Spherical trigonometry
This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
r-getopt 1.20.2 — Command-line option processor for R
This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages
argparse which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.
r-getoptlong 0.1.7 — Parsing command-line arguments and variable interpolation
This is yet another command-line argument parser which wraps the powerful Perl module
Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.
r-ggally 1.4.0 — Extension to ggplot2
The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.
r-ggbeeswarm 0.6.0 — Categorical scatter (violin point) plots
This package provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.
r-ggbio 1.28.0 — Visualization tools for genomic data
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.
r-ggdendro 0.1-20 — Create Dendrograms and Tree Diagrams Using ggplot2
This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device with out exposing the data. The ggdendro package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.
r-ggjoy 0.4.1 — Joyplots in ggplot2
Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in
r-ggmap 2.6.1 — Spatial visualization with ggplot2
This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools common to those tasks, including functions for geolocation and routing.
r-ggplot2 2.2.1 — An implementation of the grammar of graphics
Ggplot2 is an implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes.
r-ggpubr 0.1.7 — ggplot2-based publication-ready plots
The ggplot2 package is an excellent and flexible package for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.
r-ggrepel 0.8.0 — Repulsive text and label geometries for ggplot2
This package provides text and label geometries for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from the data points.
r-ggridges 0.5.0 — Ridgeline plots in ggplot2
Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in
r-ggsci 2.9 — Scientific journal and sci-fi themed color palettes for ggplot2
This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
r-ggseqlogo 0.1 — ggplot2 extension for drawing genetic sequence logos
The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.
r-ggsignif 0.4.0 — Significance brackets for ggplot2
Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting the groups of interest which itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.
r-ggthemes 3.5.0 — Extra themes, scales and geoms for
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 2.0-16 — 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 0.1.0 — 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 2.46.0 — 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
calculating and plotting two-dimensional data summaries
enhanced regression diagnostic plots
formula-enabled interface to
displaying textual data in 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 0.6.6 — 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
r-gqtlbase 1.12.0 — 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 1.12.0 — 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 1.58.0 — 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 1.14.0 — GRO-seq analysis pipeline
This package provides a pipeline for the analysis of GRO-seq data.
r-gseabase 1.42.0 — 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 3.5.0 — 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
NULL values, and many more.
r-gviz 1.24.0 — 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 2.12.0 — 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 1.6.1 — 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-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 1.8.0 — 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 1.0.0 — 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 0.14.1 — 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 0.7 — 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 1.24.0 — 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
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 1.22.2 — 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 1.2 — 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 22.214.171.124 — 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 (
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 1.2.1 — 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
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-impute 1.54.0 — Imputation for microarray data
This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging.
r-inline 0.3.15 — 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
.Call calling conventions.
r-interactionset 1.8.0 — Base classes for storing genomic interaction data
This packages provides the
ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
r-interactivedisplaybase 1.18.0 — 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 2.14.10 — 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-jomo 2.6-2 — 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 1.20.0 — 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 0.9-26 — 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-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 0.7.3 — 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 0.20-35 — 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 1.6.1 — 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 1.10.0 — 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.