Packages — R (Page 9 of 51)

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r-heatmap3 1.1.9

This package provides an improved heatmap package. It is completely compatible with the original R function `heatmap', and provides more powerful and convenient features. …

r-heatmaply 1.2.1

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 3.0.0

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-here 1.0.1

This package lets you construct paths to your project's files. Use the `here' function as a drop-in replacement for `file.path', it will always locate the files relative to your project root. …

r-hexbin 1.28.2

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

r-hiddenmarkov 1.8-13

This package contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the…

r-hierfstat 0.5-7

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-highlight 0.5.0

This package provides a syntax highlighter for R code based on the results of the R parser. It supports rendering in HTML and LaTeX markup. It includes a custom Sweave…

r-highr 0.9

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 1.36.0

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 4.5-0

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-hmm 1.0

This package provides an easy to use library to setup, apply and make inference with discrete time and discrete space hidden Markov models. …

r-hms 1.1.1

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-howmany 0.3-1

When testing multiple hypotheses simultaneously, this package provides functionality to calculate a lower bound for the number of correct rejections (as a function of the number of rejected hypotheses), which holds simultaneously -with…

r-hpar 1.34.0

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

r-hrbrthemes 0.8.0

This package provides a compilation of extra `ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. …

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 2.2.1

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 0.5.2

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

r-htmlwidgets 1.5.4

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 1.46.0

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-httpcode 0.3.0

`httpcode' provides functionality for finding and explaining the meaning of `HTTP' status codes. Functions are included for searching for codes by full or partial number, by message, and to get appropriate…

r-httpuv 1.6.3

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 1.4.2

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 1.3.5

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-hunspell 3.0.1

This package provides a low-level spell checker and morphological analyzer based on the famous `hunspell' library. The package can analyze or check individual words as well as parse text, LaTeX, HTML…

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 1.44.0

This package provides functions for visualizing hypergraphs. …

r-hypergeo 1.2-13

The Gaussian hypergeometric function for complex numbers. …

r-hypergraph 1.64.0

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

r-ibdreg 0.3.6

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-ibreakdown 2.0.1

This package provides a model agnostic tool for decomposition of predictions from black boxes. It supports additive attributions and attributions with interactions. The Break Down Table shows contributions of every…

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-icens 1.64.0

This package provides many functions for computing the "nonparametric maximum likelihood estimator" (NPMLE) for censored and truncated data. …

r-icge 0.4.1

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 1.28.0

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 1.20.0

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-ideoviz 1.28.0

This package provides functions to plot data associated with arbitrary genomic intervals along chromosomal ideogram. …

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-ids 1.0.1

This package lets you generate random or human readable and pronounceable identifiers. …

r-ifultools 2.0-22

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

r-igraph 1.2.6

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-iheatmapr 0.5.1

iheatmapr is an R package for building complex, interactive heatmaps using modular building blocks. "Complex" heatmaps are heatmaps in which subplots along the rows or columns of the main heatmap add…

r-ihw 1.20.0

"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 0.34.0

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

r-imager 0.42.10

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-iml 0.10.1

This package provides interpretability methods to analyze the behavior and predictions of any machine learning model. Implemented methods are: * Feature importance described by Fisher et al. …

r-import 1.2.0

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 1.66.0

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-infer 1.0.0

The objective of this package is to perform inference using an expressive statistical grammar that coheres with the Tidy design framework. …

r-influencer 0.1.0.1

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-ingredients 2.2.0

This is a collection of tools for assessment of feature importance and feature effects. Key functions are: * `feature_importance()' for assessment of global level feature importance, …

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 0.3.19

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 0.14.4

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 1.2.2

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 1.22.0

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 1.20.0

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 1.30.0

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

r-intergraph 2.0-2

Functions implemented in this package allow to coerce (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages `network' and `igraph'. …

r-interval 1.1-0.7

This package provides functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests. …

r-intervals 0.15.2

Tools for working with and comparing sets of points and intervals. …

r-inum 1.0-4

This package provides an enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames. …

r-invgamma 1.1

This package provides a light weight implementation of the standard distribution functions for the inverse gamma distribution, wrapping those for the gamma distribution in the `stats' package. …

r-ioniser 2.16.0

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 0.9-12

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 2.26.0

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 1.0

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 1.2

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-irtoys 0.2.1

This package provides a collection of functions useful in learning and practicing "Item Response Theory" (IRT), which can be combined into larger programs. It provides basic CTT analysis, a simple common…

r-iso 0.0-18.1

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

r-isoband 0.2.5

This package provides a fast C++ implementation to generate contour lines (isolines) and contour polygons (isobands) from regularly spaced grids containing elevation data. …

r-isocodes 2021.02.24

This package provides ISO language, territory, currency, script and character codes. It provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217 currency codes, ISO 15924 script codes, and the…

r-iterators 1.0.13

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-janeaustenr 0.1.5

This package provides the full texts for Jane Austen's six completed novels, ready for text analysis. These novels are "Sense and Sensibility", "Pride and Prejudice", "Mansfield Park", "Emma", "Northanger Abbey", and…

r-jomo 2.7-2

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 0.1-9

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-jquerylib 0.1.4

Obtain any major version of jQuery and use it in any webpage generated by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't need to use this package directly,…

r-jsonlite 1.7.2

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 1.3.4

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-karyoploter 1.18.0

This package creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimics many R base graphics functions coupling them with…

r-kegggraph 1.52.0

`r-kegggraph' is an interface between Kegg Pathway database and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated kgml…

r-keggrest 1.32.0

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

r-kendall 2.2

This package computes the Kendall rank correlation and Mann-Kendall trend test. …

r-keras 2.6.0

This package provides an interface to Keras, a high-level neural networks API. Keras was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well…

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 2.23-20

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-keyring 1.2.0

This package provides a platform-independent API to access the operating system's credential store. It currently supports Keychain on macOS, Credential Store on Windows, the Secret Service API on GNU/Linux, and a…

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