Packages — R (Page 14 of 61)

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r-oro-nifti 0.11.4

This package provides functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle. …

r-ouch 2.18

This package provides tools to fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree. …

r-outliers 0.15

This package provides a collection of some tests commonly used for identifying outliers. …

r-overlap 0.3.4

This package provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals. …

r-packcircles 0.3.4

Algorithms to find arrangements of non-overlapping circles. …

r-packrat 0.8.1

This package provides a dependency manager for R projects that allows you to manage the R packages your project depends on in an isolated, portable, and reproducible way. …

r-pacman 0.5.1

This package provides tools to more conveniently perform tasks associated with add-on packages. `pacman' conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. …

r-paletteer 1.4.1

The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This package aims to collect all color palettes across the…

r-palmerpenguins 0.1.1

This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data…

r-pamr 1.56.1

This package provides some functions for sample classification in microarrays. …

r-pan 1.6

This package implements multiple imputation for multivariate panel or clustered data. …

r-pander 0.6.5

The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex…

r-paradox 0.10.0

With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. …

r-paralleldist 0.2.6

This package provides a fast parallelized alternative to R's native `dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of predefined distance functions from…

r-parallelly 1.32.1

This package provides utility functions that enhance the `parallel' package and support the built-in parallel backends of the `future' package. For example, `availableCores' gives the number of CPU cores available to…

r-parameters 0.18.2

This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like…

r-parathyroidse 1.34.0

This package provides `RangedSummarizedExperiment' objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The sequencing was performed on tumor…

r-parcor 0.2-6

This package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso…

r-parmigene 1.1.0

This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks. …

r-parsedate 1.3.0

This package provides three functions for dealing with dates: `parse_iso_8601' recognizes and parses all valid ISO 8601 date and time formats, `parse_date' parses dates in unspecified formats, and `format_iso_8601' formats a date…

r-parsnip 1.0.1

This package provides a common interface to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. R, Spark, Stan,…

r-partitions 1.10-7

This package provides tools to enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given. …

r-partykit 1.2-16

This package provides a toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. …

r-pasilla 1.24.0

This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article 'Conservation of an RNA regulatory map between Drosophila and mammals' by…

r-pastecs 1.3.21

This package provides functions for regulation, decomposition and analysis of space-time series. The `pastecs' library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R. …

r-patchwork 1.1.2

The `ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API…

r-pathview 1.36.1

`r-pathview' is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to…

r-paws 0.1.12

This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service. …

r-paws-analytics 0.1.12

This package provides an interface to Amazon Web Services analytics services, including Elastic MapReduce Hadoop and Spark big data service, Elasticsearch search engine, and more. …

r-paws-application-integration 0.1.12

This package provides an interface to Amazon Web Services application integration services, including Simple Queue Service (SQS) message queue, Simple Notification Service (SNS) publish/subscribe messaging, and more. …

r-paws-common 0.5.0

This package provides functions for making low-level API requests to Amazon Web Services. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build…

r-paws-compute 0.1.13

This package provides an interface to Amazon Web Services compute services, including Elastic Compute Cloud (EC2), Lambda functions-as-a-service, containers, batch processing, and more. …

r-paws-cost-management 0.1.12

This package provides an interface to Amazon Web Services cost management services, including cost and usage reports, budgets, pricing, and more. …

r-paws-customer-engagement 0.1.12

This package provides an interface to Amazon Web Services customer engagement services, including Simple Email Service, Connect contact center service, and more. …

r-paws-database 0.1.12

This package provides an interface to Amazon Web Services database services, including Relational Database Service (RDS), DynamoDB NoSQL database, and more. …

r-paws-developer-tools 0.1.12

This package provides an interface to Amazon Web Services developer tools services, including version control, continuous integration and deployment, and more. …

r-paws-end-user-computing 0.1.12

This package provides an interface to Amazon Web Services end user computing services, including collaborative document editing, mobile intranet, and more. …

r-paws-machine-learning 0.1.12

This package provides an interface to Amazon Web Services machine learning services, including SageMaker managed machine learning service, natural language processing, speech recognition, translation, and more. …

r-paws-management 0.1.12

This package provides an interface to Amazon Web Services management and governance services, including CloudWatch application and infrastructure monitoring, Auto Scaling for automatically scaling resources, and more. …

r-paws-networking 0.1.12

This package provides an interface to Amazon Web Services networking and content delivery services, including Route 53 Domain Name System service, CloudFront content delivery, load balancing, and more. …

r-paws-security-identity 0.1.12

This package provides an interface to Amazon Web Services security, identity, and compliance services, including the Identity and Access Management (IAM) service for managing access to services and resources, and more. …

r-paws-storage 0.1.12

This package provides an interface to Amazon Web Services storage services, including Simple Storage Service (S3). …

r-pbapply 1.5-0

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap. …

r-pbdmpi 0.4-4

This package provides an efficient interface to MPI by utilizing S4 classes and methods with a focus on "Single Program/Multiple Data" (SPMD) parallel programming style, which is intended for batch parallel execution. …

r-pbdzmq 0.3-7

ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. The main focus is on…

r-pbivnorm 0.6.0

This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF. …

r-pbkrtest 0.5.1

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models. …

r-pbmcapply 1.5.1

This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the `mc*apply' family. …

r-pcaexplorer 2.22.0

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates…

r-pcamethods 1.88.0

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA,…

r-pcapp 2.0-2

This package provides functions for robust "principal component analysis" (PCA) by projection pursuit. …

r-pcatools 2.8.0

"Principal Component Analysis" (PCA) extracts the fundamental structure of the data without the need to build any model to represent it. This "summary" of the data is arrived at through a…

r-pdftools 3.3.0

This package provides utilities based on `libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF…

r-pdist 1.2.1

Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling `dist',…

r-pegas 1.1

This package provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage…

r-penalized 0.9-52

This package provides tools for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge)…

r-perfmeas 1.2.5

This package implements different performance measures for classification and ranking tasks. "Area under curve" (AUC), precision at a given recall, F-score for single and multiple classes are available. …

r-performance 0.9.2

This package provides utilities for computing measures to assess model quality, which are not directly provided by R's `base' or `stats' packages. These include e.g. measures like r-squared, intraclass correlation…

r-performanceanalytics 2.0.4

This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. …

r-perm 1.0-0.2

This package provides several methods for performing permutation tests. It has three main functions, to perform linear permutation tests. These tests are tests where the test statistic is the sum…

r-permute 0.9-7

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). `permute' also allows split-plot designs,…

r-pfam-db 3.15.0

This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories. …

r-phangorn 2.10.0

Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. …

r-phantompeakqualtools 1.2.2-1.8d2b2d1

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these…

r-phastcons100way-ucsc-hg19 3.7.2

This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species. …

r-pheatmap 1.0.12

This package provides an implementation of heatmaps that offers more control over dimensions and appearance. …

r-philentropy 0.6.0

This package computes optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics…

r-phontools 0.2-2.1

This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the…

r-phyclust 0.1-30

"Phylogenetic clustering" (phyloclustering) is an evolutionary continuous time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package `phyclust' provides a convenient implementation of phyloclustering…

r-phylobase 0.8.10

This package provides a base `S4' class for comparative methods, incorporating one or more trees and trait data. …

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 1.40.0

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

r-phylotools 0.2.2

This package provides a collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers. …

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 1.8.1

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 2.0.6

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 1.3.0

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 1.68.0

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 2.8-1

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 1.9.6

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 1.1.20

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

r-polychrome 1.5.1

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. …

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