Packages — R (Page 16 of 61)

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r-rappdirs 0.3.3

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 (https://github.com/ActiveState/appdirs)…

r-rapportools 1.1

This package provides helper functions that act as wrappers to more advanced statistical methods with the advantage of having sane defaults for quick reporting. …

r-raremetals2 0.1

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…

r-rarpack 0.11-0

This package was previously an R wrapper of the ARPACK library, and now a shell of the R package RSpectra, an R interface to the Spectra library for solving large scale eigenvalue/vector…

r-raster 3.6-3

The package implements basic and high-level functions for reading, writing, manipulating, analyzing and modeling of gridded spatial data. Processing of very large files is supported. …

r-rastervis 0.51.2

This package provides methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides…

r-rbamtools 2.16.17

This package provides an R interface to functions of the SAMtools library. …

r-rbenchmark 1.0.0

This `r-rbenchmark' package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a…

r-rbgl 1.72.0

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

r-rbibutils 2.2.9

This package converts between a number of bibliography formats, including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils utilities and supports all bibliography formats and character encodings implemented…

r-rbiofabric 0.3-1.666c2ae

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-rbokeh 0.5.2

This package provides a native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library (https://bokeh.pydata.org/). …

r-rbowtie 1.36.0

This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. …

r-rbowtie2 2.2.0

This package provides an R wrapper of the popular `bowtie2' sequencing reads aligner and `AdapterRemoval', a convenient tool for rapid adapter trimming, identification, and read merging. …

r-rcas 1.22.0

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-rcdd 1.5

This package converts back and forth between two representations of a convex polytope: as solution of a set of linear equalities and inequalities and as convex hull of set of points and…

r-rcistarget 1.16.0

RcisTarget identifies "transcription factor binding motifs" (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the "transcription start site"…

r-rcmdcheck 1.4.0

Run `R CMD check' from R programmatically, and capture the results of the individual checks. …

r-rcolorbrewer 1.1-3

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

r-rcpp 1.0.9

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…

r-rcppalgos 2.6.0

This package provides optimized functions and flexible combinatorial iterators implemented in C++ for solving problems in combinatorics and computational mathematics. It utilizes the `RMatrix' class from `RcppParallel' for thread safety. There…

r-rcppannoy 0.0.19

Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from and save to disk. This package provides an R…

r-rcpparmadillo 0.11.2.4.0

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…

r-rcppeigen 0.3.3.9.2

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,…

r-rcppgsl 0.3.11

The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface…

r-rcpphnsw 0.4.1

Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package. …

r-rcppml 0.3.7

This package provides fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices. …

r-rcppnumerical 0.4-0

This package provides a collection of libraries for numerical computing (numerical integration, optimization, etc.) and their integration with `Rcpp'. …

r-rcppparallel 5.1.5

This package provides high level functions for parallel programming with Rcpp. For example, the `parallelFor()' function can be used to convert the work of a standard serial `for' loop into a parallel…

r-rcppprogress 0.4.2

This package displays 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

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…

r-rcppthread 2.1.3

This package provides a C++11-style thread class and thread pool that can safely be interrupted from R. …

r-rcpptoml 0.1.7

The TOML configuration format specifies an excellent format suitable for both human editing as well as the common uses of a machine-readable format. This package provides Rcpp bindings to a TOML…

r-rcppxptrutils 0.1.2

This package provides the means to compile user-supplied C++ functions with Rcpp and retrieve an `XPtr' that can be passed to other C++ components. …

r-rcppziggurat 0.1.6

The Ziggurat generator for normally distributed random numbers, originally proposed by Marsaglia and Tsang (2000, `https://doi.org/10.18637/jss.v005.i08') has been improved upon a few times starting with Leong et al (2005, `https://doi.org/10.18637/jss.v012.i07'). This package…

r-rcurl 1.98-1.8

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. …

r-rda 1.0.2-2.1

This package provides tools for shrunken centroids regularized discriminant analysis for the purpose of classifying high dimensional data. …

r-rdpack 2.4

This package provides functions for manipulation of R documentation objects, including functions `reprompt()' and `ereprompt()' for updating Rd documentation for functions, methods and classes; it also includes Rd macros for citations and import…

r-reactome-db 1.70.0

This package provides a set of annotation maps for the REACTOME database, assembled using data from REACTOME. …

r-reactomepa 1.40.0

This package provides functions for pathway analysis based on the REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. …

r-readbitmap 0.1.5

This package provides tools to identify and read BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than…

r-readods 1.7.0

Import "OpenDocument Spreadsheet" (ODS) into R as a data frame. Also support writing data frame into ODS file. …

r-readr 2.1.2

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

r-readtext 0.81

This package provides functions for importing and handling text files and formatted text files with additional meta-data, such including `.csv', `.tab', `.json', `.xml', `.html', `.pdf', `.doc', `.docx', `.rtf', `.xls', `.xlsx', and others. …

r-readxl 1.4.1

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 1.0.1

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…

r-refgenome 1.7.7

This package contains functionality for importing and managing of downloaded genome annotation data from the Ensembl genome browser (European Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and…

r-refmanager 1.3.0

This package provides tools for importing and working with bibliographic references. It greatly enhances the `bibentry' class by providing a class `BibEntry' which stores BibTeX and BibLaTeX references, supports UTF-8 encoding, and…

r-reghelper 1.1.1

This package provides a set of functions used to automate commonly used methods in regression analysis. This includes plotting interactions, and calculating simple slopes, standardized coefficients, regions of significance (Johnson & Neyman,…

r-regioner 1.28.0

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 0.5-1

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

r-regsem 1.9.3

This package uses both ridge and lasso penalties (and extensions) to penalize specific parameters in structural equation models. The package offers additional cost functions, cross validation, and other extensions beyond traditional structural…

r-reinforcelearn 0.2.1

This package implements reinforcement learning environments and algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm can be used with function approximation, eligibility traces (Singh & Sutton, 1996) and…

r-reldist 1.7-1

This package provides tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the…

r-rematch 1.0.1

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-rematch2 2.1.2

This package provides wrappers on `regexpr' and `gregexpr' to return the match results in tidy data frames. …

r-remoter 0.4-0

This package provides a set of utilities for client/server computing with R, controlling a remote R session (the server) from a local one (the client). …

r-remotes 2.4.2

Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the `install_*' functions in the `devtools' package. Indeed…

r-rentrez 1.2.3

This package provides an R interface to the NCBI's EUtils API, allowing users to search databases like GenBank PubMed, process the results of those searches and pull data into their R sessions. …

r-renv 0.15.5

This package provides a dependency management toolkit for R. Using renv, you can create and manage project-local R libraries, save the state of these libraries to a lockfile, and later restore…

r-reordercluster 2.0

This package provides tools for performing the leaf reordering for the dendrogram that preserves the hierarchical clustering result and at the same time tries to group instances from the same class together. …

r-reportingtools 2.36.0

The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may…

r-reportr 1.3.0

This package provides a system for reporting messages, which offers certain useful features over the standard R system, such as the incorporation of output consolidation, message filtering, assertions, expression substitution, automatic generation of…

r-repr 1.1.4

This package provides string and binary representations of objects for several formats and MIME types. …

r-reprex 2.0.2

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…

r-reqon 1.42.0

This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. …

r-reshape 0.8.9

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

r-reshape2 1.4.4

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

r-residualmatrix 1.6.1

This package implements tools for delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. It also supports partial computation of residuals…

r-restfulr 0.0.15

This package models a RESTful service as if it were a nested R list. …

r-restrserve 1.2.1

RestRserve is an R web API framework for building high-performance AND robust microservices and app backends. With Rserve backend on UNIX-like systems it is parallel by design. It will handle…

r-reticulate 1.26

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…

r-revgeo 0.15

The `revgeo' procedure allows you to use the Photon geocoder for OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with minimal hassle. …

r-rex 1.2.1

This package provides a friendly interface for the construction of regular expressions. Regular expressions are a very powerful feature, however they are often difficult to interpret. Rex allows you to…

r-rfast 2.0.6

This package provides a collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic,…

r-rffc 1.0

This package provides functions for extracting feature contributions from a random forest model from package `randomForest'. Feature contributions provide detailed information about the relationship between data variables and the predicted value returned…

r-rfigshare 0.3.8

This package provides an interface to figshare, a scientific repository to archive and assign DOIs to data, software, figures, and more. …

r-rgadem 2.44.1

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. …

r-rgdal 1.5-32

This package provides bindings to the Geospatial Data Abstraction Library (GDAL) and access to projection/transformation operations from the PROJ.4 library. …

r-rgeos 0.5-9

This package provides an R interface to Geometry Engine (GEOS) using the C API for topology operations on geometries. …

r-rgexf 0.16.2

Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). It allows the user to easily build/read graph files including attributes, GEXF visual attributes (such…

r-rgl 0.109.6

This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (`plot3d()', etc.) as well as functions for constructing representations of geometric objects (`cube3d()', etc.). …

r-rglpk 0.6-4

This package provides an R interface to the GNU Linear Programming Kit, software for solving large-scale "linear programming" (LP), "mixed integer linear programming" (MILP) and other related problems. …

r-rgooglemaps 1.4.5.3

This package serves two purposes: 1. Provide a comfortable R interface to query the Google server for static maps, and 2. Use the map…

r-rgraphviz 2.40.0

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

r-rgreat 1.28.0

This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server. …

r-rhdf5 2.40.0

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…

r-rhdf5filters 1.8.0

This package provides a collection of compression filters for use with HDF5 datasets. …

r-rhdf5lib 1.18.2

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

r-rhisat2 1.12.0

This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform…

r-rhpcblasctl 0.21-247.1

This package allows you to control the number of threads the BLAS library uses. It is also possible to control the number of threads in OpenMP. …

r-rhtslib 1.28.0

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 1.26.0

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…

r-riboseqr 1.30.0

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

r-rintrojs 0.3.2

This package provides a wrapper for the Intro.js (http://www.introjs.com) library. This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static…

r-rio 0.5.29

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…

r-ripseeker 1.26.0

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…

r-rismed 2.3.0

This package provides a set of tools to extract bibliographic content from the National Center for Biotechnology Information (NCBI) databases, including PubMed. The name RISmed is a portmanteau of RIS (for…

r-riverplot 0.10

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…

r-rjags 4-13

This package provides an R interface to the JAGS MCMC library. JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain…

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