Packages — R (Page 11 of 32)
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r-quadprog 1.5-8
This package contains routines and documentation for solving quadratic programming problems. …
r-quanteda 2.1.1
This package provides a fast, flexible, and comprehensive framework for quantitative text analysis in R. It provides functionality for corpus management, creating and manipulating tokens and ngrams, exploring keywords in context, forming…
r-quantmod 0.4.17
This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies. …
r-quantreg 5.61
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…
r-quantro 1.22.0
This package provides a data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such…
r-quasr 1.28.0
This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control…
r-quic 1.1
This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation…
r-qvalue 2.20.0
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…
r-r-cache 0.14.0
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…
r-r-devices 2.16.1
This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as…
r-r-filesets 2.13.0
This package provides classes and methods to locate, setup, subset, navigate and iterate file sets, i.e. sets of files located in one or more directories on the file system. The…
r-r-huge 0.9.0
This is a deprecated package for accessing huge amounts of data. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was…
r-r-methodss3 1.8.0
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…
r-r-oo 1.23.0
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…
r-r-rsp 0.44.0
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()%>'. …
r-r-utils 2.9.2
This package provides utility functions useful when programming and developing R packages. …
r-r2glmm 0.1.2
This package computes model and semi partial R squared with confidence limits for the linear and generalized linear mixed model (LMM and GLMM). The R squared measure from L. J.…
r-r2html 2.3.2
This package includes HTML functions and methods to write in an HTML file. Thus, making HTML reports is easy. It includes a function that allows redirection on the fly, which…
r-r4rna 0.1.4
The R4RNA package aims to be a general framework for the analysis of RNA secondary structure and comparative analysis in R. …
r-r6 2.4.1
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…
r-radiant-data 1.3.10
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
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-randomizr 0.20.0
This package provides tools for generating random assignments for common experimental designs and random samples for common sampling designs. …
r-randtoolbox 1.30.1
This package provides 1. pseudo random generators, such as general linear congruential generators, multiple recursive generators and generalized feedback shift register …
r-ranger 0.12.1
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…
r-rann 2.6.1
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…
r-rann-l1 2.5.2
This package provides tools to find the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. There is support…
r-rapidjsonr 1.2.0
This package provides JSON parsing capability through the Rapidjson library. …
r-rappdirs 0.3.1
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 1.0
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 3.3-13
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-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 1.64.0
This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library. …
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-rbowtie 1.28.0
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 1.10.0
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 1.14.0
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 1.2-2
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 1.8.0
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 1.3.3
Run `R CMD check' from R programmatically, and capture the results of the individual checks. …
r-rcolorbrewer 1.1-2
This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org …
r-rcpp 1.0.5
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-rcppannoy 0.0.16
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 0.9.900.2.0
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 0.3.3.7.0
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 0.3.8
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 0.2.0
Hnswlib is a C++ library for approximate nearest neighbors. This package provides a minimal R interface by relying on the Rcpp package. …
r-rcppparallel 5.0.2
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-rcppziggurat 0.1.5
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 1.95-0.1.2
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 1.0.0
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 1.32.0
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-readr 1.3.1
This package provides functions to read flat or tabular text files from disk (or a connection). …
r-readxl 1.3.1
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 0.1.13
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 1.2.12
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-regioner 1.20.1
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 1.5.2
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-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 2.2.0
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-renv 0.11.0
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 1.0
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 2.28.0
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 1.1.0
This package provides string and binary representations of objects for several formats and MIME types. …
r-reprex 0.3.0
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 1.34.0
This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. …
r-reshape 0.8.8
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-reticulate 1.16
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-rex 1.2.0
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 1.9.9
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-rgadem 2.36.0
rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. …
r-rgdal 1.5-16
This package provides bindings to the Geospatial Data Abstraction Library (GDAL) and access to projection/transformation operations from the PROJ.4 library. …
r-rgl 0.100.54
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 2.32.0
This package interfaces R with the graphviz library for plotting R graph objects from the `graph' package. …
r-rgreat 1.20.0
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 2.32.2
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-rhdf5lib 1.10.1
This package provides C and C++ HDF5 libraries for use in R packages. …
r-rhisat2 1.4.0
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 0.20-137
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 1.20.0
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 1.18.0
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 1.22.0
This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments. …
r-rintrojs 0.2.2
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…