Packages — R (Page 2 of 9)

r-crayon 1.3.4 — Colored terminal output for R

Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the "chalk" JavaScript project.

r-crosstalk 1.0.0 — Inter-widget interactivity for HTML widgets

This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). It currently supports linked brushing and filtering.

r-cubature 1.3-11 — Adaptive multivariate integration over hypercubes

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both hcubature and pcubature routines in addition to a vector interface.

r-curl 3.2 — HTTP client for R

The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption, gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.

r-cvst 0.2-1 — Fast cross-validation via sequential testing

This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

r-data-table 1.10.4-3 — Enhanced version of data.frame R object

The R package data.table is an extension of data.frame providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.

r-dbi 0.8 — R database interface

The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

r-dbplyr 1.2.1 — Dplyr back end for databases

This package provides a dplyr back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a DBI back end; more advanced features require SQL translation to be provided by the package author.

r-ddalpha 1.3.2 — Depth-Based classification and calculation of data depth

This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.

r-debugme 1.1.0 — Debug R packages

This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.

r-delayedarray 0.4.1 — Delayed operations on array-like objects

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.

r-delayedmatrixstats 1.0.3 — Functions that apply to rows and columns of DelayedMatrix objects

This package provides a port of the matrixStats API for use with DelayedMatrix objects from the DelayedArray package. It contains high-performing functions operating on rows and columns of DelayedMatrix objects, e.g. colMedians, rowMedians, colRanks, rowRanks, colSds, and rowSds. Functions are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

r-dendextend 1.7.0 — Extending 'dendrogram' functionality in R

This package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.

r-deoptimr 1.0-8 — Differential evolution optimization in pure R

This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language.

r-desc 1.1.1 — Manipulate DESCRIPTION Files

This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.

r-deseq 1.30.0 — Differential gene expression analysis

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

r-deseq2 1.18.1 — Differential gene expression analysis

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

r-desolve 1.20 — Solvers for initial value problems of differential equations

This package provides functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.

r-devtools 1.13.5 — Tools to make developing R packages easier

The devtools package is a collection of package development tools to simplify the devolpment of R packages.

r-dexseq 1.24.4 — Inference of differential exon usage in RNA-Seq

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

r-dichromat 2.0-0 — Color schemes for dichromats

Dichromat collapses red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

r-diffusionmap 1.1-0 — Diffusion map

This package implements the diffusion map method of data parametrization, including creation and visualization of diffusion maps, clustering with diffusion K-means and regression using the adaptive regression model.

r-digest 0.6.15 — Create cryptographic hash digests of R objects

This package contains an implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code.

Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

r-dimred 0.1.0 — Framework for dimensionality reduction

This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.

r-diptest 0.75-7 — Hartigan's dip test statistic for unimodality

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.

r-directlabels 2017.03.31 — Direct labels for multicolor plots

This package provides an extensible framework for automatically placing direct labels onto multicolor plots. Label positions are described using positioning methods that can be re-used across several different plots. There are heuristics for examining trellis and ggplot objects and inferring an appropriate positioning method.

r-dirichletmultinomial 1.20.0 — Dirichlet-Multinomial mixture models for microbiome data

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

r-distillery 1.0-4 — Functions for confidence intervals and object information

This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.

r-diversitree 0.9-10 — Comparative 'phylogenetic' analyses of diversification

This package contains a number of comparative "phylogenetic" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of "BiSSE" (Binary State Speciation and Extinction) and its unresolved tree extensions, "MuSSE" (Multiple State Speciation and Extinction), "QuaSSE", "GeoSSE", and "BiSSE-ness" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.

r-dnacopy 1.52.0 — Implementation of a circular binary segmentation algorithm

This package implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

r-domc 1.3.5 — Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

r-doparallel 1.0.11 — Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the parallel package.

r-dosnow 1.0.16 — Foreach parallel adaptor for the snow package

This package provides a parallel backend for the %dopar% function using the snow package.

r-dplyr 0.7.4 — Tools for working with data frames in R

dplyr is the next iteration of plyr. It is focussed on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.

r-dropbead 0-2.d746c6f — Basic exploration and analysis of Drop-seq data

This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.

r-drr 0.0.3 — Dimensionality reduction via regression

This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.

r-dt 0.4 — R wrapper of the DataTables JavaScript library

This package allows for data objects in R to be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package.

r-dtw 1.18-1 — Dynamic Time Warping Algorithms

This package provides a comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on.

r-dyn 0.2-9.6 — Time series regression

This package provides the dyn class interfaces ts, irts, zoo and zooreg time series classes to lm, glm, loess, quantreg::rq, MASS::rlm, MCMCpack::MCMCregress(), quantreg::rq(), randomForest::randomForest() and other regression functions, allowing those functions to be used with time series including specifications that may contain lags, diffs and missing values.

r-dynamictreecut 1.63-1 — Detect clusters in hierarchical clustering dendrograms

This package contains methods for the detection of clusters in hierarchical clustering dendrograms.

r-e1071 1.6-8 — Miscellaneous functions for probability theory

This package provides functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, and more.

r-edaseq 2.12.0 — Exploratory data analysis and normalization for RNA-Seq

This package provides support for numerical and graphical summaries of RNA-Seq genomic read data. Provided within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization. Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization.

r-edger 3.20.9 — EdgeR does empirical analysis of digital gene expression data

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

r-emdbook 1.3.9 — Support functions and data for "Ecological Models and Data"

This package provides auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

r-energy 1.7-2 — Multivariate inference via the energy of data

This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.

r-ensembldb 2.2.2 — Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript-centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package also provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

r-erma 0.10.1 — Epigenomic road map adventures

The epigenomics road map describes locations of epigenetic marks in DNA from a variety of cell types. Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin. This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.

r-estimability 1.3 — Tools for assessing estimability of linear predictions

Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly.

r-evaluate 0.10.1 — Parsing and evaluation tools for R

This package provides tools that allow you to recreate the parsing, evaluation and display of R code, with enough information that you can accurately recreate what happens at the command line. The tools can easily be adapted for other output formats, such as HTML or LaTeX.

r-expm 0.999-2 — Tools for matrix exponentials and related quantities

This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.

r-extradistr 1.8.8 — Additional univariate and multivariate distributions

This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.

r-extremes 2.0-8 — Extreme value analysis

ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.

r-fail 1.3 — File abstraction interface layer (FAIL)

This package provides a more comfortable interface to work with R data or source files in a key-value fashion.

r-fastcluster 1.1.24 — Fast hierarchical clustering routines

This package implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package scipy.cluster.hierarchy, hclust() in R's stats package, and the flashClust package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.

r-fastica 1.2-1 — FastICA algorithms to perform ICA and projection pursuit

This package provides an implementation of the FastICA algorithm to perform independent component analysis (ICA) and projection pursuit.

r-fastmatch 1.1-0 — Fast match function

This package provides a fast match replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.

r-fastseg 1.24.0 — Fast segmentation algorithm for genetic sequencing data

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

r-fdrtool 1.2.15 — Estimation of false discovery rates and higher criticism

This package provides tools to estimate tail area-based false discovery rates as well as local false discovery rates for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.

r-feather 0.3.1 — R Bindings to the Feather API

Read and write feather files, a lightweight binary columnar daa store designed for maximum speed.

r-ff 2.2-13 — Memory-efficient storage of large data on disk and access functions

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

r-ffbase 0.12.3 — Basic statistical functions for package 'ff'

This package extends the out of memory vectors of ff with statistical functions and other utilities to ease their usage.

r-fit-models 0.5-14 — Compare fitted models

The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to compare robustly and classically fitted model objects. The aim of the fit.models package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.

r-fitdistrplus 1.0-9 — Fitting a parametric distribution from data

This package extends the fitdistr function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.

r-fithic 1.4.0 — Confidence estimation for intra-chromosomal contact maps

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

r-fivethirtyeight 0.1.0 — Data and code behind the stories at FiveThirtyEight

This R package provides access to the code and data sets published by the statistics blog FiveThirtyEight.

r-flexmix 2.3-14 — Flexible mixture modeling

This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.

r-fnn 1.1 — Fast nearest neighbor search algorithms and applications

This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.

r-forcats 0.3.0 — Tools for working with factors

This package provides helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, "anonymizing", and manually "recoding").

r-foreach 1.4.4 — Foreach looping construct for R

This package provides support for the foreach looping construct. foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

r-foreign 0.8-69 — Read data stored by other statistics software

This package provides functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.

r-formatr 1.5 — Format R code automatically

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

r-formula 1.2-2 — Extended model formulas

This package provides a new class Formula, which extends the base class formula. It supports extended formulas with multiple parts of regressors on the right-hand side and/or multiple responses on the left-hand side.

r-fpc 2.1-11 — Flexible procedures for clustering

This package provides various methods for clustering and cluster validation. For example, it provides fixed point clustering, linear regression clustering, clustering by merging Gaussian mixture components, as well as symmetric and asymmetric discriminant projections for visualisation of the separation of groupings.

r-fractal 2.0-4 — Fractal time series modeling and analysis

This package provides tools for stochastic fractal and deterministic chaotic time series analysis.

r-futile-logger 1.4.3 — Logging utility for R

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

r-futile-options 1.0.1 — Options management framework

The futile.options subsystem provides an easy user-defined options management system that is properly scoped. This means that options created via futile.options are fully self-contained and will not collide with options defined in other packages.

r-gage 2.28.2 — Generally applicable gene-set enrichment for pathway analysis

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. The gage package provides functions for basic GAGE analysis, result processing and presentation. In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

r-gclus 1.3.1 — Clustering graphics

This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of pairs and parcoord which color panels according to their merit level.

r-gdata 2.18.0 — Various R programming tools for data manipulation

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

  • medical unit conversions

  • combining objects

  • character vector operations

  • factor manipulation

  • obtaining information about R objects

  • manipulating MS-Excel formatted files

  • generating fixed-width format files

  • extricating components of date and time objects

  • operations on columns of data frames

  • matrix operations

  • operations on vectors and data frames

  • value of last evaluated expression

  • wrapper for sample that ensures consistent behavior for both scalar and vector arguments

r-gdtools 0.1.7 — Utilities for graphical rendering

The gdtools package provides functionalities to get font metrics and to generate base64 encoded string from raster matrix.

r-genefilter 1.60.0 — Filter genes from high-throughput experiments

This package provides basic functions for filtering genes from high-throughput sequencing experiments.

r-geneplotter 1.56.0 — Graphics functions for genomic data

This package provides functions for plotting genomic data.

r-genomation 1.11.3 — Summary, annotation and visualization of genomic data

This package provides a package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.

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 1.14.0 — 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 1.14.2 — 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 1.30.3 — 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 1.14.0 — 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-genomicranges 1.30.3 — 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 optparse or argparse which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.

r-getoptlong 0.1.6 — 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 1.3.2 — 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 1.26.1 — 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 0.4.0 — 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 ggplot2.

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.