Packages — R (Page 7 of 33)

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r-ggvis 0.4.5

This package is a data visualization package for R providing an implementation of an interactive grammar of graphics, taking the best parts of ggplot2, combining them with the reactive framework of Shiny…

r-gh 1.1.0

This package provides a minimal R client to access the GitHub API. …

r-git2r 0.27.1

This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods. …

r-gkmsvm 0.81.0

This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel. …

r-glasso 1.11

This is a package for estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter. …

r-glimma 1.16.0

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular…

r-glmmtmb 1.0.2.1

Fit linear and generalized linear mixed models with various extensions, including zero-inflation. The models are fitted using maximum likelihood estimation via the Template Model Builder. Random effects are assumed to…

r-glmnet 4.0-2

The glmnet package provides efficient procedures for fitting the entire lasso or elastic-net regularization path for linear and Poisson regression, as well as logistic, multinomial, Cox, multiple-response Gaussian and grouped multinomial models. …

r-globaloptions 0.1.2

This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private. …

r-globals 0.12.5

This package provides tools to identify global ("unknown" or "free") objects in R expressions by code inspection using various strategies, e.g. conservative or liberal. The objective of this package is…

r-glue 1.4.2

This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals. …

r-gmodels 2.18.1

This package provides various R programming tools for model fitting. …

r-gmp 0.6-0

This package supports multiple precision arithmetic (big integers and rationals, prime number tests, matrix computation), "arithmetic without limitations" using the GNU Multiple Precision library. …

r-go-db 3.7.0

The purpose of this GO.db annotation package is to provide detailed information about the latest version of the Gene Ontologies. …

r-goftest 1.2-2

This package provides Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit for continuous univariate distributions, using efficient algorithms. …

r-gofuncr 1.8.0

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (`Homo.sapiens' by default); the GO-graph is included in the…

r-googlesheets 0.3.0

This package provides tools to interact with Google Sheets from within R. …

r-goplot 1.0.2

This package provides an implementation of multilayered visualizations for enhanced graphical representation of functional analysis data. It combines and integrates omics data derived from expression and functional annotation enrichment analyses. Its…

r-gosemsim 2.14.1

The semantic comparisons of "Gene Ontology" (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R…

r-goseq 1.40.0

This package provides tools to detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. …

r-gostats 2.54.0

This package provides a set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations. …

r-gower 0.2.2

This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP. …

r-gpfit 1.0-8

This package provides a computationally stable approach of fitting a "Gaussian Process" (GP) model to a deterministic simulator. …

r-gplots 3.0.4

This package provides various R programming tools for plotting data, including: * calculating and plotting locally smoothed summary function * enhanced versions of standard plots …

r-gprofiler 0.7.0

This package provides tools for functional enrichment analysis, gene identifier conversion and mapping homologous genes across related organisms via the `g:Profiler' toolkit. …

r-gprofiler2 0.2.0

This package provides a toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via g:Profiler (https://biit.cs.ut.ee/gprofiler). The main tools are: 1. `g:GOSt', functional enrichment…

r-gqtlbase 1.20.0

The purpose of this package is to simplify the storage and interrogation of "quantitative trait loci" (QTL) archives, such as eQTL, mQTL, dsQTL, and more. …

r-gqtlstats 1.20.0

This package provides tools for the computationally efficient analysis of "quantitative trait loci" (QTL) data, including eQTL, mQTL, dsQTL, etc. The software in this package aims to support refinements and functional interpretation…

r-graph 1.66.0

This package implements some simple graph handling capabilities for R. …

r-graphite 1.34.0

Graphite provides networks derived from eight public pathway databases, and automates the conversion of node identifiers (e.g. from Entrez IDs to gene symbols). …

r-graphlayouts 0.7.0

This package provides several layout algorithms to visualize networks which are not part of the igraph library. Most are based on the concept of stress majorization by Gansner et al. …

r-gridbase 0.4-7

This package provides an integration of base and grid graphics for R. …

r-gridextra 2.3

This package provides a number of user-level functions to work with `grid' graphics, notably to arrange multiple grid-based plots on a page, and draw tables. …

r-gridgraphics 0.5-0

This package provides functions to convert a page of plots drawn with the `graphics' package into identical output drawn with the `grid' package. The result looks like the original `graphics'-based plot,…

r-grimport 0.9-3

This package provides functions for converting, importing, and drawing PostScript pictures in R plots. …

r-grimport2 0.2-0

This package provides functions for importing external vector images and drawing them as part of R plots. This package is different from the `grImport' package because, where that package imports PostScript…

r-grohmm 1.22.0

This package provides a pipeline for the analysis of GRO-seq data. …

r-grouped 0.6-0

This package provides regression models for grouped and coarse data, under the coarsened at random assumption. …

r-grr 0.9.5

This package provides alternative implementations of some base R functions, including `sort', `order', and `match'. The functions are simplified but can be faster or have other advantages. …

r-gseabase 1.50.1

This package provides classes and methods to support "Gene Set Enrichment Analysis" (GSEA). …

r-gsl 2.1-6

This package provides an R wrapper for the special functions and quasi random number generators of the GNU Scientific Library. …

r-gsubfn 0.7

This package provides `gsubfn' which is like `gsub' but can take a replacement function or certain other objects instead of the replacement string. Matches and back references are input to the…

r-gtable 0.3.0

Gtable is a collection of tools to make it easier to work with "tables" of grobs. …

r-gtools 3.8.2

This package contains a collection of various functions to assist in R programming, such as tools to assist in developing, updating, and maintaining R and R packages, calculating the logit and inverse…

r-gtrellis 1.20.1

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects.…

r-gviz 1.32.0

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 2.20.1

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 1.2-8

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 1.8.5

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 0.1.4

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 1.6.6

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 2.2.6.1

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 2.3.1

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

r-hdf5array 1.16.1

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

r-hdf5r 1.3.3

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 1.1.1

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 2.34.0

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 1.28.1

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 0.5-7

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-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 1.32.0

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 4.4-1

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-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 1.30.0

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 2.0.1

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 0.5.0

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 1.42.0

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 1.5.4

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 1.3.4.1

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

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 1.40.0

This package provides functions for visualizing hypergraphs. …

r-hypergraph 1.60.0

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

r-ibdreg 0.3.1

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 1.3.1

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 1.60.0

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

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 1.24.0

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 1.16.0

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 1.24.0

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-ifultools 2.0-5

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

r-igraph 1.2.5

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 0.5.0

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 1.16.0

"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 0.30.0

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

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