Packages — R (Page 10 of 25)

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r-pore 0.24

This package provides graphical user interfaces to organize and visualize Nanopore sequencing data. …

r-powerlaw 0.70.2

This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used…

r-powerplus 3.1

This package provides tools for the computation of matrix and scalar exponentiation. …

r-ppls 1.6-1.1

This package contains linear and nonlinear regression methods based on partial least squares and penalization techniques. Model parameters are selected via cross-validation, and confidence intervals ans tests for the regression coefficients can…

r-prabclus 2.3-2

This package provides distance-based parametric bootstrap tests for clustering with spatial neighborhood information. It implements some distance measures, clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based…

r-pracma 2.2.9

This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting. …

r-praise 1.0.0

This package provides template functions to assist in building friendly R packages that praise their users. …

r-prediction 0.3.14

This package provides the `prediction()' function, a type-safe alternative to `predict()' that always returns a data frame. The package currently supports common model types (e.g., `"lm"', `"glm"') from the `stats' package,…

r-preprocesscore 1.48.0

This package provides a library of core pre-processing and normalization routines. …

r-preseqr 4.0.0

This package can be used to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When…

r-prettyunits 1.1.1

This package provides tools for pretty, human readable formatting of quantities. …

r-proc 1.16.1

This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap.…

r-processx 3.4.2

This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status…

r-prodlim 2019.11.13

This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods. …

r-progeny 1.8.0

This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression". …

r-progress 1.2.2

This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS…

r-promises 1.1.0

This package provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also…

r-protgenerics 1.18.0

This package provides S4 generic functions needed by Bioconductor proteomics packages. …

r-proto 1.0.0

Proto is an object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas. …

r-protviz 0.6.0

This package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich, where…

r-proxy 0.4-23

This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones. …

r-proxyc 0.1.5

This package provides efficient tools to compute the proximity between rows or columns of large matrices. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. …

r-prroc 1.3.1

This package computes the areas under the "precision-recall" (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the…

r-pryr 0.1.4

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

r-ps 1.3.2

The ps package implements an API to list, query, and manipulate system processes. Most of its code is based on the `psutil' Python package. …

r-pscl 1.5.2

The `pscl' is an R package providing classes and methods for: 1. Bayesian analysis of roll call data (item-response models); 2. elementary Bayesian statistics; 3. maximum likelihood…

r-psiplot 2.3.0

PSIplot is an R package for generating plots of "percent spliced-in" (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are…

r-psych 1.9.12.31

This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and…

r-purrr 0.3.3

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

r-pwr 1.2-2

This package provides power analysis functions along the lines of Cohen (1988). …

r-qap 0.1-1

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

r-qdnaseq 1.22.0

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…

r-qgraph 1.6.5

This package implements tools for weighted network visualization and analysis, as well as Gaussian graphical model computation. It contains graph plotting methods, and tools for psychometric data visualization and graphical model estimation.…

r-qlcmatrix 0.9.7

This package provides an extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for the special…

r-qqman 0.1.4

This package allows you to create Q-Q and Manhattan plots for GWAS data from PLINK results. …

r-qtl 1.45-11

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…

r-qtl2 0.20

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs. …

r-quadprog 1.5-8

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

r-quanteda 1.5.2

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 0.4-15

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

r-quantreg 5.54

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 1.20.0

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 1.26.0

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 2.18.0

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 0.43.2

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 1.0.6

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-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 1.1

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 3.0-12

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 1.62.1

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 1.26.0

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 1.8.0

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 1.12.0

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-rcistarget 1.6.0

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 1.0.3

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 0.0.14

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 0.9.850.1.0

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 0.3.7

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 4.4.4

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 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…

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-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 0.11-1

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 1.30.0

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 0.1.9

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 1.18.1

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

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