Packages — R (Page 10 of 61)

### Packages menu:

#### Browse alphabetically

### r-guitar 2.12.0

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site. …

### r-guix-install 1.0.0

This R package provides a single procedure `guix.install()', which allows users to install R packages via Guix right from within their running R session. If the requested R package does not…

### r-gutils 0.2.0-1.10e36c7

This is an R package providing additional capabilities and speed for `GenomicRanges' operations. …

### r-gviz 1.40.1

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC…

### r-gwascat 2.28.1

This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog. …

### r-h5 0.9.9

This package provides an S4 interface to the HDF5 library supporting fast storage and retrieval of R-objects like vectors, matrices and arrays to binary files in a language independent format. The…

### r-hapassoc 1.2-9

Hapassoc performs likelihood inference of trait associations with haplotypes and other covariates in "generalized linear models" (GLMs). The functions are developed primarily for data collected in cohort or cross-sectional studies. They can…

### r-haplo-stats 1.8.9

This package provides routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of…

### r-hardhat 1.2.0

Building modeling packages is hard. A large amount of effort generally goes into providing an implementation for a new method that is efficient, fast, and correct, but often less emphasis is…

### r-hardyweinberg 1.7.5

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 0.1

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 2.2.6.2

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 2.5.1

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

### r-hdf5array 1.24.1

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

### r-hdf5r 1.3.6

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-hdrcde 3.4

This is a package for the computation of highest density regions in one and two dimensions, kernel estimation of univariate density functions conditional on one covariate, and multimodal regression. …

### 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 1.3.0

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 3.4.0

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-hgu133plus2-db 3.13.0

This package provides Affymetrix HG-U133_Plus_2 array annotation data (chip hgu133plus2) assembled using data from public repositories. …

### 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 0.5-11

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 1.40.0

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 4.7-1

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 1.0.1

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 1.1.2

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-homologene 1.4.68.19.3.27

This package provides a wrapper for the homologene database by the National Center for Biotechnology Information (NCBI). It allows searching for gene homologs across species. The package also includes an…

### 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 1.38.0

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 1.16.0

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 2.4.1

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 0.5.3

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 1.50.0

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 2.0.10

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 1.6.6

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 1.4.4

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 3.0.2

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 1.3.2.1

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

### r-hyperdraw 1.48.0

This package provides functions for visualizing hypergraphs. …

### r-hypergeo 1.2-13

The Gaussian hypergeometric function for complex numbers. …

### r-hypergraph 1.68.0

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 1.0-3

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

### r-icellnet 1.0-0.b9c0548

This package provides a a transcriptomic-based framework to dissect cell communication in a global manner. It integrates an original expert-curated database of ligand-receptor interactions taking into account multiple subunits expression. Based…

### r-icens 1.68.0

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 1.32.0

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 1.24.1

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 1.32.0

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 1.3

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 2.0-26

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

### r-igraph 1.3.4

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 1.24.0

"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 0.38.0

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

### r-imager 0.42.13

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 0.11.1

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 1.3.0

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 1.70.0

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 1.0.3

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

### r-infercnv 1.12.0

`InferCNV' is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of…

### 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 1.2.0.1

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 0.18.3

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 1.26.0

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 1.24.0

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 1.34.0

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 coercing (i.e. convert) network data between classes provided by other R packages. Currently supported classes are those defined in packages `network' and `igraph'. …

### r-interp 1.1-3

Bivariate data interpolation on regular and irregular grids, either linear or using splines are the main part of this package. It is intended to provide replacement functions for the ACM licensed…

### r-interval 1.1-0.8

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 2.20.0

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-iotools 0.3-2

This package provides basic I/O tools for streaming and data parsing. …

### r-ipred 0.9-13

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-ips 0.0.11

This package provides functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states. …

### r-iranges 2.30.1

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 1.1

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. …