Packages — R (Page 8 of 51)

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r-ggbeeswarm 0.6.0

This package provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting. …

r-ggbio 1.40.0

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics…

r-ggcorrplot 0.1.3

The ggcorrplot package can be used to visualize easily a correlation matrix using ggplot2. It provides a solution for reordering the correlation matrix and displays the significance level on the plot.…

r-ggcyto 1.20.0

With the dedicated fortify method implemented for `flowSet', `ncdfFlowSet' and `GatingSet' classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The `ggcyto' wrapper and some custom…

r-ggdendro 0.1.22

This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots…

r-ggeffects 1.1.1

This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the `ggplot2' package. …

r-ggextra 0.9

This package is a collection of functions and layers to enhance ggplot2. The flagship function is `ggMarginal()', which can be used to add marginal histograms/boxplots/density plots to ggplot2 scatterplots. …

r-ggforce 0.3.3

The aim of the ggplot2 package is to aid in visual data investigations. This focus has led to a lack of facilities for composing specialized plots. This package aims to…

r-ggformula 0.10.1

The `r-ggformula' introduces a family of graphics functions, gf_point(), gf_density(), and so on, bring the formula interface to ggplot(). This captures and extends the excellent simplicity of the lattice-graphics formula interface, while…

r-ggfortify 0.4.12

This package provides unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis. The package offers a single plotting interface for these analysis…

r-ggfun 0.0.4

This package provides useful functions to edit ggplot object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends). …

r-ggh4x 0.2.0

This package is a `ggplot2' extension. It provides some utility functions that do not entirely fit within the grammar of graphics concept. The package extends `ggpplots' facets through customisation, by…

r-ggjoy 0.4.1

Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in `ggplot2'. …

r-ggm 2.5

This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models. …

r-ggmap 3.0.0

This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps). It includes tools…

r-ggnetwork 0.5.10

This package provides geometries to plot network objects with the ggplot2 package. …

r-ggnewscale 0.4.5

This package lets you use multiple fill and color scales in ggplot2. …

r-ggplot-multistats 1.0.0

This package provides the ggplot binning layer `stat_summaries_hex()', which functions similar to its singular form, but allows the use of multiple statistics per bin. Those statistics can be mapped to multiple…

r-ggplot2 3.3.5

Ggplot2 is an implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can…

r-ggplotify 0.1.0

This package provides tools to convert plot function calls (using expression or formula) to `grob' or `ggplot' objects that are compatible with the `grid' and `ggplot2' environment. With this package, we…

r-ggpmisc 0.4.3

This package provides extensions to `ggplot2', respecting the grammar of its graphics paradigm. …

r-ggpointdensity 0.1.0

This package provides a cross between a 2D density plot and a scatter plot, implemented as a ggplot2 `geom'. Points in the scatter plot are colored by the number of neighboring…

r-ggpp 0.4.2

This package contains extensions to ggplot2. 1. Geomas: `geom_table', `geom_plot' and `geom_grob' add insets to plots using native data coordinates, while `geom_table_npc', `geom_plot_npc' and …

r-ggpubr 0.4.0

The ggplot2 package is an excellent and flexible package for elegant data visualization in R. However the default generated plots require some formatting before we can send them for publication. …

r-ggraph 2.0.5

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. The ggraph package is an extension…

r-ggrepel 0.9.1

This package provides text and label geometries for ggplot2 that help to avoid overlapping text labels. Labels repel away from each other and away from the data points. …

r-ggridges 0.5.3

Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in `ggplot2'. …

r-ggsci 2.9

This package provides a collection of ggplot2 color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows. …

r-ggseqlogo 0.1

The range of functions provided by this package makes it possible to draw highly versatile genomic sequence logos. Features include, but are not limited to, modifying colour schemes and fonts used…

r-ggsignif 0.6.3

Enrich your ggplots with group-wise comparisons. This package provides an easy way to indicate if two groups are significantly different. Commonly this is shown by a bracket on top connecting…

r-ggstance 0.3.5

This package is a `r-ggplot2' extension that provides flipped components: 1. horizontal versions of `r-ggplot2' stats and `r-ggplot2' geoms; 2. vertical versions of `r-ggplot2' positions. …

r-ggtext 0.1.1

This package provides a ggplot2 extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported. …

r-ggthemes 4.2.4

This package provides extra themes and scales for `ggplot2' that replicate the look of plots by Edward Tufte and Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The Wall Street Journal,…

r-ggtree 3.0.4

This package extends the ggplot2 plotting system which implements a grammar of graphics. ggtree is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data. …

r-ggvis 0.4.7

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 1.3.0

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

r-git2r 0.28.0

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

r-gitcreds 0.1.1

Query, set, and delete credentials from the git credential store. Manage GitHub tokens and other git credentials. This package is to be used by other packages that need to authenticate…

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 2.2.0

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-glinternet 1.0.12

Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates…

r-glmmtmb 1.1.2.3

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 4.1-2

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 0.14.0

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 0.6-2

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 1.12.0

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-googledrive 2.0.0

This package lets you manage Google Drive files from R. …

r-googlesheets 0.3.0

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

r-googlesheets4 1.0.0

This package lets you interact with Google Sheets through the Sheets API v4 (https://developers.google.com/sheets/api). This package can read and write both the metadata and the cell data in a Sheet. …

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 2.18.1

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 1.44.0

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 2.58.0

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 3.1.1

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 0.2.1

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 1.21.1

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 1.21.3

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 1.70.0

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

r-graphite 1.38.0

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 0.7.1

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-greylistchip 1.24.0

This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. …

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 0.5-1

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-gridtext 0.1.4

This package provides support for rendering of formatted text using Grid graphics. Text can be formatted via a minimal subset of Markdown, HTML, and inline CSS directives, and it can be…

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 1.26.0

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-gsa 1.03.1

This package lets you determine the significance of pre-defined sets of genes with respect to an outcome variable, such as a group indicator, a quantitative variable or a survival time. …

r-gseabase 1.54.0

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

r-gsl 2.1-7

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 3.9.2

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 1.24.0

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-guitar 2.8.0

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-gviz 1.36.2

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 2.24.0

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 1.8.7

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 0.1.6

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 1.7.2

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 2.4.3

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

r-hdf5array 1.20.0

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

r-hdf5r 1.3.4

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. …

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