Packages — R (Page 7 of 24)

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r-hardyweinberg 1.6.3

This package contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are included in the package, as well…

r-harmony 1.0-1.4d16538

This package provides an implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al `doi.org/10.1101/461954'. The package includes a standalone Harmony function and interfaces to external frameworks. …

r-hash 2.2.6.1

This package implements a data structure similar to hashes in Perl and dictionaries in Python but with a purposefully R flavor. For objects of appreciable size, access using hashes outperforms native…

r-haven 2.2.0

This package lets you mport foreign statistical formats into R via the embedded ReadStat (https://github.com/WizardMac/ReadStat) C library. …

r-hdf5array 1.14.1

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing. …

r-hdf5r 1.3.1

HDF5 is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the HDF5 API…

r-heatmaply 1.0.0

This package enables you to create interactive cluster heatmaps that can be saved as a stand-alone HTML file, embedded in R Markdown documents or in a Shiny app, and made available in…

r-heatplus 2.32.0

This package provides tools to display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a…

r-hexbin 1.28.0

This package provides binning and plotting functions for hexagonal bins. It uses and relies on grid graphics and formal (S4) classes and methods. …

r-hierfstat 0.04-22

This package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions…

r-highr 0.8

This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package. …

r-hitc 1.30.0

The HiTC package was developed to explore high-throughput "C" data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis…

r-hmisc 4.3-0

This package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character…

r-hms 0.5.3

This package implements an S3 class for storing and formatting time-of-day values, based on the `difftime' class. …

r-homo-sapiens 1.3.1

This package contains the Homo.sapiens object to access data from several related annotation packages. …

r-hpar 1.28.0

This package provides a simple interface to and data from the Human Protein Atlas project. …

r-hsmmsinglecell 1.2.0

Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary "human skeletal muscle myoblasts" (HSMM) were expanded under high mitogen conditions (GM) and then differentiated…

r-htmltable 1.13.3

This package provides functions to build tables with advanced layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying CSS-structure is simple…

r-htmltools 0.4.0

This package provides tools for HTML generation and output in R. …

r-htmlwidgets 1.5.1

HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications. …

r-htqpcr 1.40.0

Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays…

r-htscluster 2.0.8

This package provides a Poisson mixture model is implemented to cluster genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter estimation is performed using either the EM or CEM algorithm, and the…

r-httpuv 1.5.2

The httpuv package provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather…

r-httr 1.4.1

The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs…

r-huge 1.3.4

This package provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline. …

r-hwde 0.67

This package fits models for genotypic disequilibria, as described in Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast terms are available that account for first order interactions…

r-hwriter 1.3.2

This package provides easy-to-use and versatile functions to output R objects in HTML format. …

r-hyperdraw 1.38.0

This package provides functions for visualizing hypergraphs. …

r-hypergraph 1.58.0

This package implements some simple capabilities for representing and manipulating hypergraphs. …

r-ibdreg 0.2.5

This package provides a method to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative…

r-ica 1.0-2

This package provides tools for "Independent Component Analysis" (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and "Joint Approximate Diagonalization of Eigenmatrices" (JADE). …

r-icge 0.3

ICGE is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than…

r-iclusterplus 1.22.0

iClusterPlus is developed for integrative clustering analysis of multi-type genomic data and is an enhanced version of iCluster proposed and developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise…

r-icobra 1.14.0

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results. …

r-idpmisc 1.1.20

This package provides different high-level graphics functions for displaying large datasets, displaying circular data in a very flexible way, finding local maxima, brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with…

r-idr 1.2

This is a package for estimating the copula mixture model and plotting correspondence curves in "Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by…

r-ifultools 2.0-5

This package provides C code used by the wmtsa, fractal, and sapa R packages. …

r-igraph 1.2.4.2

This package provides routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and…

r-ihw 1.14.0

"Independent hypothesis weighting" (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW…

r-illuminahumanmethylation450kanno-ilmn12-hg19 0.6.0

This package provides manifests and annotation for Illumina's 450k array data. …

r-illuminahumanmethylationepicmanifest 0.3.0

This is a manifest package for Illumina's EPIC methylation arrays. …

r-illuminaio 0.28.0

This package provides tools for parsing Illumina's microarray output files, including IDAT. …

r-imager 0.41.2

This is a package for fast image processing for images in up to 4 dimensions (two spatial dimensions, one time/depth dimension, one color dimension). It provides most traditional image processing tools…

r-import 1.1.0

This is an alternative mechanism for importing objects from packages. The syntax allows for importing multiple objects from a package with a single command in an expressive way. The import…

r-impute 1.60.0

This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging. …

r-imputeyn 1.3

This package allows for the imputation of the last largest censored observantions. This method brings less bias and more efficient estimates for AFT models. …

r-ineq 0.2-13

This package provides tools for measuring inequality, concentration, and poverty measures. It provides both empirical and theoretical Lorenz curves. …

r-influencer 0.1.0

This package provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and "effective…

r-infotheo 1.2.0

This package implements various measures of information theory based on several entropy estimators. …

r-ini 0.3.1

This package provides tools to parse simple `.ini' configuration files to an structured list. Users can manipulate this resulting list with `lapply()' functions. This same structured list can be used…

r-inline 0.3.15

This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting `.C' and `.Call' calling conventions. …

r-insight 0.8.0

This package provides a tool to provide an easy, intuitive and consistent access to information contained in various R models, like model formulas, model terms, information about random effects, data that was…

r-insol 1.2.1

This package provides functions to compute insolation on tilted surfaces, computes atmospheric transmittance and related parameters such as: Earth radius vector, declination, sunset and sunrise, daylength, equation of time, vector in the direction…

r-inspect 1.16.2

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that…

r-interactionset 1.14.0

This package provides the `GInteractions', `InteractionSet' and `ContactMatrix' objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments. …

r-interactivedisplaybase 1.24.0

This package contains the basic methods needed to generate interactive Shiny-based display methods for Bioconductor objects. …

r-ioniser 2.10.0

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base…

r-ipred 0.9-9

This package provides improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error. …

r-iranges 2.20.2

This package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as `Vector' objects),…

r-irdisplay 0.7.0

This package provides an interface to the rich display capabilities of Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a running IRkernel session. …

r-irkernel 1.1

The R kernel for the Jupyter environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network. …

r-irlba 2.3.3

This package provides fast and memory efficient methods for truncated singular and eigenvalue decompositions, as well as for principal component analysis of large sparse or dense matrices. …

r-iso 0.0-18

This package provides support for linear order and unimodal order (univariate) isotonic regression and bivariate isotonic regression with linear order on both variables. …

r-iterators 1.0.12

This package provides support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data. …

r-itertools 0.1-3

This package provides various tools for creating iterators, many patterned after functions in the Python `itertools' module, and others patterned after functions in the snow package. …

r-jomo 2.6-10

Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation http://doi.org/10.1002/9781119942283 (Carpenter and Kenward (2013)). Novel aspects of jomo are the possibility of handling binary and categorical…

r-jpeg 0.1-8.1

This package provides a way to read, write and display bitmap images stored in the JPEG format with R. It can read and write both files and in-memory raw vectors. …

r-jsonlite 1.6

The jsonlite package provides a fast JSON parser and generator optimized for statistical data and the web. It offers flexible, robust, high performance tools for working with JSON in R and…

r-kableextra 1.1.0

Build complex HTML or LaTeX tables using `kable()' from `knitr' and the piping syntax from `magrittr'. The function `kable()' is a light weight table generator coming from `knitr'. This package…

r-keggrest 1.26.1

This package provides a package that provides a client interface to the "Kyoto Encyclopedia of Genes and Genomes" (KEGG) REST server. …

r-kernelfactory 0.3.0

Kernel factory is an ensemble method where each base classifier (random forest) is fit on the kernel matrix of a subset of the training data. …

r-kernlab 0.9-29

This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods `kernlab' includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes…

r-kernsmooth 2.23-16

This package provides functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing". …

r-knitr 1.27

This package provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques. …

r-knitrbootstrap 1.0.2

This package provides a framework to create Bootstrap 3 HTML reports from knitr Rmarkdown. …

r-knn-covertree 1.0

Similarly to the FNN package, this package allows calculation of the k nearest neighbors (kNN) of a data matrix. The implementation is based on cover trees introduced by Alina Beygelzimer, Sham…

r-kohonen 3.0.10

This package provides functions to train "self-organising maps" (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen,…

r-ks 1.11.6

This package provides kernel smoothers for univariate and multivariate data, including density functions, density derivatives, cumulative distributions, modal clustering, discriminant analysis, and two-sample hypothesis testing. …

r-ksamples 1.2-9

This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic,…

r-labeling 0.3

The labeling package provides a range of axis labeling algorithms. …

r-laeken 0.5.0

This package provides tools for the estimation of indicators on social exclusion and poverty, as well as an implementation of Pareto tail modeling for empirical income distributions. …

r-lambda-r 1.2.4

This package provides a language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety. …

r-lars 1.2

Least Angle Regression ("LAR") is a model selection algorithm; a useful and less greedy version of traditional forward selection methods. A simple modification of the LAR algorithm implements Tibshirani's Lasso; the…

r-lassopv 0.2.0

This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path…

r-later 1.0.0

This package provides tools to execute arbitrary R or C functions some time after the current time, after the R execution stack has emptied. …

r-lattice 0.20-38

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also…

r-latticeextra 0.6-29

Building on the infrastructure provided by the lattice package, this package provides several new high-level graphics functions and methods, as well as additional utilities such as panel and axis annotation functions. …

r-lava 1.6.6

This package provides tools for the estimation and simulation of latent variable models. …

r-lavaan 0.6-5

This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models. …

r-lazyeval 0.2.2

This package provides the tools necessary to do non-standard evaluation (NSE) in R. …

r-lda 1.4.2

This package implements "latent Dirichlet allocation" (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is…

r-ldblock 1.16.0

This package defines data structures for "linkage disequilibrium" (LD) measures in populations. Its purpose is to simplify handling of existing population-level data for the purpose of flexibly defining LD blocks. …

r-ldheatmap 0.99-7

This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map…

r-leaps 3.1

This package provides tools for regression subset selection, including exhaustive search. …

r-learnbayes 2.15.1

This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions.…

r-learnr 0.10.0

This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages. …

r-leiden 0.3.2

This package implements the Python `leidenalg' module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al…

r-lemon 0.4.3

This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions. …

r-lhs 1.0.1

This package provides a number of methods for creating and augmenting Latin Hypercube Samples. …

r-libcoin 1.0-5

This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999). …

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