Packages — R (Page 9 of 24)

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r-nleqslv 3.3.2

The `r-nleqslv' package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are…

r-nlme 3.1-143

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models. …

r-nloptr 1.2.1

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available…

r-nlp 0.2-0

This package provides basic classes and methods for Natural Language Processing. …

r-nmf 0.21.0

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and…

r-nnet 7.3-12

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models. …

r-nnls 1.4

This package provides an R interface to the Lawson-Hanson implementation of an algorithm for "non-negative least squares" (NNLS). It also allows the combination of non-negative and non-positive constraints. …

r-noiseq 2.30.0

This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type…

r-nonnest2 0.5-2

This package allows for testing of non-nested models. It includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. The package…

r-nor1mix 1.3-0

This package provides S3 classes and methods for one-dimensional normal mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also…

r-nortest 1.0-4

This package provides five omnibus tests for testing the composite hypothesis of normality. …

r-np 0.60-9

This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. …

r-npsurv 0.4-0

This package contains functions for non-parametric survival analysis of exact and interval-censored observations. …

r-numderiv 2016.8-1.1

This package provides methods for calculating accurate numerical first and second order derivatives. …

r-officer 0.3.6

This package provides tools to access and manipulate Word and PowerPoint documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let…

r-oligo 1.50.0

This package provides a package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). …

r-oligoclasses 1.48.0

This package contains class definitions, validity checks, and initialization methods for classes used by the `oligo' and `crlmm' packages. …

r-ontologyindex 2.5

This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms. …

r-opencyto 1.24.0

This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy. …

r-openssl 1.4.1

This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either…

r-openxlsx 4.1.4

This package simplifies the creation of Excel `.xlsx' files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to…

r-optparse 1.6.4

This package provides a command line parser inspired by Python's `optparse' library to be used with Rscript to write shebang scripts that accept short and long options. …

r-orddom 3.1

This package provides tools to compute ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under…

r-ordinal 2019.12-10

This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is…

r-ore 1.6.3

This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features. …

r-org-ce-eg-db 3.7.0

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans. …

r-org-dm-eg-db 3.7.0

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster. …

r-org-dr-eg-db 3.7.0

This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers. …

r-org-hs-eg-db 3.7.0

This package contains genome-wide annotations for Human, primarily based on mapping using Entrez Gene identifiers. …

r-org-mm-eg-db 3.7.0

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus. …

r-organismdbi 1.28.0

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select…

r-ouch 2.14-1

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

r-outliers 0.14

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

r-overlap 0.3.2

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-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 0.6.3

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-parameters 0.4.1

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-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 1.0.2

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 1.2.0

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-partitions 1.9-22

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-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 0.0.1-1.fd7958b

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-pbapply 1.4-2

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-pbdzmq 0.3-3

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 0.4-7

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 1.5.0

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

r-pcamethods 1.78.0

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 1.9-73

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

r-pdist 1.2

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 0.12

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 0.9-51

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-performance 0.4.3

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 1.5.3

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-permute 0.9-5

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 3.8.2

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

r-phangorn 2.5.5

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-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-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-physicalactivity 0.2-2

This `r-physicalactivity' package provides a function `wearingMarking' for classification of monitor 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

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 1.4.3

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

r-pixmap 0.4-11

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

r-pkgbuild 1.0.6

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-pkgload 1.0.2

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 0.31

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 1.58.0

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 1.3

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-plotly 4.9.1

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 3.7-7

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

r-pls 2.7-2

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 1.8.5

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 4.3

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-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-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 1.1.17

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

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-polynom 1.4-0

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-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 3.4.1

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…

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