Packages — R (Page 14 of 58)

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### r-phylogram 2.1.0

The `r-phylogram' package is a tool for for developing phylogenetic trees as deeply-nested lists known as "dendrogram" objects. It provides functions for conversion between "dendrogram" and "phylo" class objects, as well…

### r-phyloseq 1.38.0

Phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. …

### r-physicalactivity 0.2-4

This `r-physicalactivity' package provides a function `wearingMarking' for classification of monitored wear and nonwear time intervals in accelerometer data collected to assess physical activity. The package also contains functions for making plots…

### r-picante 1.8.2

This package provides functions for phylocom integration, community analyses, null-models, traits and evolution. It implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values…

### r-pillar 1.7.0

This package provides a `pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals. …

### r-pinfsc50 1.2.0

This package contains genomic data for the plant pathogen Phytophthora infestans. It includes a variant file, a sequence file and an annotation file. This package is intended to be used as…

### r-pixmap 0.4-12

This package provides functions for importing, exporting, plotting and other manipulations of bitmapped images. …

### r-pkgbuild 1.3.1

This package provides functions used to build R packages. It locates compilers needed to build R packages on various platforms and ensures the PATH is configured appropriately so R can use…

### r-pkgconfig 2.0.3

This package provides the functionality to set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected. …

### r-pkgdown 2.0.2

The goal of this package is to generate an attractive and useful website from a source package. `pkgdown' converts your documentation, vignettes, README file, and more to HTML making it easy…

### r-pkgload 1.2.4

This package simulates the process of installing a package and then attaching it. This is a key part of the `devtools' package as it allows you to rapidly iterate while developing…

### r-pkgmaker 0.32.2

This package provides some low-level utilities to use for R package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities. …

### r-plgem 1.66.0

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use…

### r-plogr 0.2.0

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream. …

### r-plot3d 1.4

This package provides functions for viewing 2D and 3D data, including perspective plots, slice plots, surface plots, scatter plots, etc. It includes data sets from oceanography. …

### r-plotfunctions 1.4

When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty…

### r-plotly 4.10.0

This package enables the translation of ggplot2 graphs to an interactive web-based version and/or the creation of custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs…

### r-plotrix 3.8-2

This package provides lots of plotting, various labeling, axis and color scaling functions for R. …

### r-pls 2.8-0

The pls package implements multivariate regression methods: Partial Least Squares Regression ("PLSR"), Principal Component Regression ("PCR"), and Canonical Powered Partial Least Squares ("CPPLS"). It supports: * several algorithms: the…

### r-plyr 1.8.7

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put…

### r-pmcmr 4.4

This is a deprecated package for calculating pairwise multiple comparisons of mean rank sums. This package is superseded by the novel PMCMRplus package. The PMCMR package is no longer maintained,…

### r-pmcmrplus 1.9.4

This package provides multiple pairwise tests. …

### r-png 0.1-7

This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors. …

### r-pnwcolors 0.1.0

This package provides color palettes. They are checked for colorblind accessibility from hue, saturation, and lightness value scaling using the Chroma.js Color Palette Helper. See `https://gka.github.io/palettes'. …

### r-poibin 1.5

This package provides an implementation of both the exact and approximation methods for computing the "cumulative distribution function" (CDF) of the Poisson binomial distribution. It also provides the "probability mass function" (PMF),…

### r-polspline 1.1.19

This package provides routines for the polynomial spline fitting routines hazard regression, hazard estimation with flexible tails, logspline, lspec, polyclass, and polymars. …

### r-polychrome 1.3.1

This package provides tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) `https://doi:10.18637/jss.v090.c01'. …

### r-polyclip 1.10-0

This package provides an R port of the library Clipper. It performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. It…

### r-polycor 0.8-1

This package provides tools to compute polychoric and polyserial correlations by quick "two-step" methods or ML, optionally with standard errors; tetrachoric and biserial correlations are special cases. …

### r-polynom 1.4-1

This package provides a collection of functions to implement a class for univariate polynomial manipulations. …

### r-pore 0.24

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

### r-posterior 1.2.1

This package provides useful tools for both users and developers of packages for fitting Bayesian models or working with output from Bayesian models. The primary goals of the package are to: …

### r-powerlaw 0.70.6

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-ppcor 1.1

This package provides users not only with a function to readily calculate the higher-order partial and semi-partial correlations but also with statistics and p-values of the correlation coefficients. …

### 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 2.3.8

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-precrec 0.12.9

This package provides tools for accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves. …

### 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 1.56.0

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

### r-prereg 0.6.0

This package provides a collection of templates to author preregistration documents for scientific studies in PDF format. …

### 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-presto 1.0.0-0.052085d

This package performs a fast Wilcoxon rank sum test and auROC analysis. …

### r-prettyunits 1.1.1

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

### r-princurve 2.1.6

This package provides procedures for fitting a principal curve to a data matrix in arbitrary dimensions. …

### r-proc 1.18.0

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 3.5.3

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-profilemodel 0.6.1

This package provides tools that can be used to calculate, evaluate, plot and use for inference the profiles of *arbitrary* inference functions for arbitrary `glm'-like fitted models with linear predictors. More…

### r-progeny 1.16.0

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-progressr 0.10.0

This package provides a minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can…

### r-projpred 2.1.1

This package performs projection predictive feature selection for generalized linear models and generalized linear and additive multilevel models. The package is compatible with the `rstanarm' and `brms' packages, but other reference models…

### r-promises 1.2.0.1

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 1.26.0

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-protolite 2.1.1

This package provides pure C++ implementations for reading and writing several common data formats based on Google protocol-buffers. It currently supports `rexp.proto' for serialized R objects, `geobuf.proto' for binary geojson, and `mvt.proto'…

### r-protviz 0.7.3

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 0.4-26

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 0.2.4

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 0.1.5

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

### r-ps 1.6.0

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 1.5.5

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 2.2.3

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-puniform 0.2.5

This package provides meta-analysis methods that correct for publication bias and outcome reporting bias. Four methods and a visual tool are currently included in the package. 1. The p-uniform method…

### r-pupillometryr 0.0.4

This package provides a unified pipeline to clean, prepare, plot, and run basic analyses on pupillometry experiments. …

### r-purrr 0.3.4

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

### r-pvclust 2.2-0

This package provides an implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)…

### r-pwr 1.3-0

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-qdapregex 0.7.2

This package provides a collection of regular expression tools associated with the `qdap' package that may be useful outside of the context of discourse analysis. Tools include removal/extraction/replacement of abbreviations, dates, dollar…

### r-qdnaseq 1.30.0

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-qgam 1.3.4

This package provides smooth additive quantile regression models, fitted using the methods of Fasiolo et al. (2017). Differently from `quantreg', the smoothing parameters are estimated automatically by marginal loss minimization, while…

### r-qgraph 1.9.2

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-qpcr 1.4-1

This is a package for model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR). …

### r-qpdf 1.1

Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the `qpdf' C++ API and does not require any command line utilities. Note…

### r-qqman 0.1.8

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

### r-qs 0.25.3

This package provides functions for quickly writing and reading any R object to and from disk. …

### r-qtl 1.50

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 0.28

This package provides a set of tools to perform "Quantitative Trait Locus" (QTL) analysis in experimental crosses. It is a reimplementation of the `R/qtl' package to better handle high-dimensional data and…

### r-quadprog 1.5-8

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

### r-qualv 0.3-4

This package provides qualitative methods for the validation of dynamic models. It contains 1. an orthogonal set of deviance measures for absolute, relative and ordinal scale…

### r-quanteda 3.2.1

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 0.4.18

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

### r-quantpsyc 1.5

Contains functions useful for data screening, testing moderation, mediation and estimating power. …

### r-quantreg 5.88

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 1.28.0

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 1.34.0

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 2.26.0

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 0.15.0

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 2.17.0

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 2.14.0

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 1.8.1

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…