Packages — R (Page 5 of 9)

r-pryr 0.1.4 — Tools for computing on the R language

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

r-psych 1.8.4 — Procedures for psychological, psychometric, and personality research

This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. The functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. It provides functions for analyzing data at multiple levels within and between group statistics, including correlations and factor analysis; functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling.

r-purrr 0.2.5 — Functional programming tools

This package completes R's functional programming tools with missing features present in other programming languages.

r-qap 0.1-1 — Heuristics for the quadratic assignment problem (QAP)

This package implements heuristics for the quadratic assignment problem (QAP). Currently only a simulated annealing heuristic is available.

r-qdnaseq 1.16.0 — Quantitative DNA sequencing for chromosomal aberrations

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

r-qtl 1.42-8 — R package for analyzing QTL experiments in genetics

R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl allows to estimate genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

r-quadprog 1.5-5 — Functions to solve quadratic programming problems

This package contains routines and documentation for solving quadratic programming problems.

r-quantmod 0.4-13 — Quantitative financial modelling framework

This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg 5.36 — Quantile regression

This package provides an estimation and inference methods for models of conditional quantiles: linear and nonlinear parametric and non-parametric models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

r-qvalue 2.12.0 — Q-value estimation for false discovery rate control

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local false discovery rate (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

r-r-cache 0.13.0 — Light-weight caching of objects and results

This package provides methods for caching or memoization of objects and results. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

r-r-methodss3 1.7.1 — S3 methods simplified

This package provides methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4.

r-r-oo 1.22.0 — R object-oriented programming with or without references

This package provides methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.

r-r-rsp 0.42.0 — Dynamic generation of scientific reports

The RSP markup language provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. Today's date is <%=Sys.Date()%>. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. RSP is ideal for self-contained scientific reports and R package vignettes.

r-r-utils 2.6.0 — Various programming utilities

This package provides utility functions useful when programming and developing R packages.

r-r4rna 0.1.4 — Analysis framework for RNA secondary structure

The R4RNA package aims to be a general framework for the analysis of RNA secondary structure and comparative analysis in R.

r-r6 2.2.2 — Classes with reference semantics in R

The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

r-radiant-data 0.9.5 — Data menu for Radiant: business analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

r-randomforest 4.6-14 — Breiman and Cutler's random forests for classification and regression

This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.

r-ranger 0.10.1 — Fast implementation of random forests

This package provides a fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently.

r-rann 2.5.1 — Fast nearest neighbour search

This package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. Provides approximate, exact searches, fixed radius searches, bd and kb trees.

r-rappdirs 0.3.1 — Determine where to save data, caches, and logs

This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's Appdirs to R.

r-raremetals2 0.1 — Analyze gene-level association tests for binary trait

The R package rareMETALS2 is an extension of the R package rareMETALS. It was designed to meta-analyze gene-level association tests for binary trait. While rareMETALS offers a near-complete solution for meta-analysis of gene-level tests for quantitative trait, it does not offer the optimal solution for binary trait. The package rareMETALS2 offers improved features for analyzing gene-level association tests in meta-analyses for binary trait.

r-rbgl 1.56.0 — Interface to the Boost graph library

This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.

r-rbiofabric 0.3-1.666c2ae — BioFabric network visualization

This package provides an implementation of the function bioFabric for creating scalable network digrams where nodes are represented by horizontal lines, and edges are represented by vertical lines.

r-rcas 1.6.0 — RNA-centric annotation system

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

r-rcolorbrewer 1.1-2 — ColorBrewer palettes

This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

r-rcpp 0.12.17 — Seamless R and C++ integration

The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.

r-rcpparmadillo 0.8.500.0 — Rcpp integration for the Armadillo linear algebra library

Armadillo is a templated C++ linear algebra library that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. This package includes the header files from the templated Armadillo library.

r-rcppeigen 0.3.3.4.0 — Rcpp integration for the Eigen templated linear algebra library

This package provides an integration of Eigen in R using a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems.

r-rcppprogress 0.4.1 — Interruptible progress bar for C++ in R packages

This package allows to display a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

r-rcpproll 0.3.0 — Efficient rolling and windowed operations

This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.

r-rcurl 1.95-0.1.2 — General network client interface for R

The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, GET and POST forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

r-readr 1.1.1 — Read tabular data

This package provides functions to read flat or tabular text files from disk (or a connection).

r-readxl 1.1.0 — Read Excel files

This package lets you import Excel files into R. It supports .xls via the embedded libxls C library and .xlsx via the embedded RapidXML C++ library.

r-recipes 0.1.3 — Preprocessing tools to create design matrices

Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

r-regioner 1.12.0 — Association analysis of genomic regions

This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

r-registry 0.5 — Infrastructure for R package registries

This package provides a generic infrastructure for creating and using R package registries.

r-rematch 1.0.1 — Match regular expressions with a nicer API

This package provides a small wrapper on regexpr to extract the matches and captured groups from the match of a regular expression to a character vector.

r-reprex 0.1.2 — Prepare reproducible R code examples for sharing

This package provides a convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. reprex also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

r-reshape 0.8.7 — Flexibly reshape data

Flexibly restructure and aggregate data using just two functions: melt and cast. This package provides them.

r-reshape2 1.4.3 — Flexibly reshape data: a reboot of the "reshape" package

Reshape2 is an R library to flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

r-reticulate 1.8 — R interface to Python

This package provides an interface from R to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types.

r-rgooglemaps 1.4.2 — Use Google Maps in R

This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.

r-rgraphviz 2.24.0 — Plotting capabilities for R graph objects

This package interfaces R with the graphviz library for plotting R graph objects from the graph package.

r-rhdf5 2.24.0 — HDF5 interface to R

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

r-rhdf5lib 1.2.1 — HDF5 library as an R package

This package provides C and C++ HDF5 libraries for use in R packages.

r-rhtslib 1.12.1 — High-throughput sequencing library as an R package

This package provides the HTSlib C library for high-throughput nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

r-riboprofiling 1.10.0 — Ribosome profiling data analysis

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

r-riboseqr 1.14.0 — Analysis of sequencing data from ribosome profiling experiments

This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.

r-rio 0.5.10 — Swiss-army knife for data I/O

This package provides streamlined data import and export infrastructure by making assumptions that the user is probably willing to make: import and export determine the data structure from the file extension, reasonable defaults are used for data import and export (e.g., stringsAsFactors=FALSE), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, convert, provides a simple method for converting between file types.

r-ripseeker 1.20.0 — Identifying protein-associated transcripts from RIP-seq experiments

This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

r-riverplot 0.6 — Sankey or ribbon plots

Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For example, they can be used to compare different clusterings. This package provides an implementation of Sankey plots for R.

r-rjson 0.2.20 — JSON library for R

This package provides functions to convert R objects into JSON objects and vice-versa.

r-rlang 0.2.1 — Functions for base types, core R and Tidyverse features

This package provides a toolbox for working with base types, core R features like the condition system, and core Tidyverse features like tidy evaluation.

r-rmarkdown 1.10 — Convert R Markdown documents into a variety of formats

This package provides tools to convert R Markdown documents into a variety of formats.

r-rmpi 0.6-7 — R interface to message-passing interface (MPI)

This package provides an interface (wrapper) to MPI APIs. It also provides an interactive R manager and worker environment.

r-rmtstat 0.3 — Distributions, statistics and tests derived from random matrix theory

This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices.

r-rmysql 0.10.15 — Database interface and MySQL driver for R

This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern MySQL client based on Rcpp is available from the RMariaDB package.

r-rngtools 1.3.1 — Utility functions for working with random number generators

This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

r-robust 0.4-18 — Port of the S+ "Robust Library"

This package is a port of the S+ "Robust Library". It provides methods for robust statistics, notably for robust regression and robust multivariate analysis.

r-robustbase 0.93-0 — Basic robust statistics

This packages allows to analyze data with robust methods such as regression methodology including model selections and multivariate statistics.

r-rocr 1.0-7 — Visualizing the performance of scoring classifiers

ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism.

r-rook 1.1-1 — Web server interface for R

This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a call method or an R closure that takes exactly one argument, an environment, and returns a list with three named elements: the status, the headers, and the body.

r-roxygen2 6.0.1 — In-source documentation system for R

Roxygen2 is a Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE files.

r-rpart 4.1-13 — Recursive partitioning and regression trees

This package provides recursive partitioning functions for classification, regression and survival trees.

r-rprojroot 1.3-2 — Finding files in project subdirectories

This package helps accessing files relative to a project root. It provides helpers for robust, reliable and flexible paths to files below a project root. The root of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

r-rrcov 1.4-4 — Scalable robust estimators with high breakdown Point

This package provides an implementation of robust location and scatter estimation and robust multivariate analysis with high breakdown point.

r-rsamtools 1.32.0 — Interface to samtools, bcftools, and tabix

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

r-rsofia 1.1 — Port of sofia-ml to R

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking.

r-rsolnp 1.16 — General non-linear optimization

The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a sequential quadratic programming (SQP) based solver).

r-rsqlite 2.1.1 — SQLite interface for R

This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.8.2) is included.

r-rstudioapi 0.7 — Safely access the RStudio API

This package provides functions to access the RStudio API and provide informative error messages when it's not available.

r-rtracklayer 1.40.3 — R interface to genome browsers and their annotation tracks

rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

r-rtsne 0.13 — T-distributed stochastic neighbor embedding

This package provides an R wrapper around the fast T-distributed Stochastic Neighbor Embedding using a Barnes-Hut implementation.

r-runit 0.4.32 — R unit test framework

This package provides R functions implementing a standard unit testing framework, with additional code inspection and report generation tools.

r-rversions 1.0.3 — Query R versions, including 'r-release' and 'r-oldrel'

This package provides functions to query the main R repository to find the versions that r-release and r-oldrel refer to, and also all previous R versions and their release dates.

r-rvest 0.3.2 — Simple web scraping for R

r-rvest helps you scrape information from web pages. It is designed to work with magrittr to make it easy to express common web scraping tasks, inspired by libraries like BeautifulSoup.

r-s4vectors 0.18.3 — S4 implementation of vectors and lists

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself.

r-sapa 2.0-2 — Spectral analysis for physical applications

This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993.

r-scales 0.5.0 — Scale functions for visualization

This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.

r-scater 1.8.0 — Single-cell analysis toolkit for gene expression data in R

This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.

r-scatterplot3d 0.3-41 — 3D scatter plot

This package provides an implementation of scatter plots for plotting. a three dimensional point cloud.

r-scran 1.8.2 — Methods for single-cell RNA-Seq data analysis

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

r-sdmtools 1.1-221 — Species distribution modelling tools

This packages provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time. It further includes methods for visualizing outcomes, selecting thresholds, calculating measures of accuracy and landscape fragmentation statistics, etc.

r-segmented 0.5-3.0 — Regression models with breakpoints estimation

Given a regression model, segmented updates the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.

r-selectr 0.4-1 — Translate CSS selectors to XPath expressions

r-selectr translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. Also provided are convenience functions useful for using CSS selectors on XML nodes. This package is a port of the Python package cssselect.

r-sendmailr 1.2-1 — Send email using R

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R.

r-seqgl 1.1.4 — Group lasso for Dnase/ChIP-seq data

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

r-seqinr 3.4-5 — Biological sequences retrieval and analysis

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.

r-seqlogo 1.46.0 — Sequence logos for DNA sequence alignments

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

r-seqminer 6.0 — Read nucleotide sequence data (VCF, BCF, and METAL formats)

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.

r-seqpattern 1.12.0 — Visualising oligonucleotide patterns and motif occurrences

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

r-seriation 1.2-3 — Infrastructure for ordering objects using seriation

This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT).

r-servr 0.10 — Simple HTTP server to serve static files or dynamic documents

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

r-seurat 2.3.2 — Seurat is an R toolkit for single cell genomics

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

r-sfsmisc 1.1-2 — Utilities from "Seminar fuer Statistik" ETH Zurich

This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics.

r-shape 1.4.4 — Functions for plotting graphical shapes

This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

r-shiny 1.1.0 — Easy interactive web applications with R

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

r-shinyace 0.3.1 — Ace editor bindings for Shiny

This package provides Ace editor bindings to enable a rich text editing environment within Shiny.