Packages — R (Page 6 of 24)

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r-gdata 2.18.0

This package provides various R programming tools for data manipulation, including: * medical unit conversions * combining objects * character vector operations *…

r-gdina 2.7.8

This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) `doi:10.1007/s11336-011-9207-7' and its extensions, including…

r-gdsfmt 1.22.0

This package provides a high-level R interface to CoreArray "Genomic Data Structure" (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information.…

r-gdtools 0.2.1

The `gdtools' package provides functionalities to get font metrics and to generate base64 encoded string from raster matrix. …

r-gee 4.13-20

This package provides a solver for generalized estimation equations. …

r-genalg 0.2.0

This package provides an R based genetic algorithm for binary and floating point chromosomes. …

r-genefilter 1.68.0

This package provides basic functions for filtering genes from high-throughput sequencing experiments. …

r-genelendatabase 1.18.0

This package provides the lengths of mRNA transcripts for a number of genomes and gene ID formats, largely based on the UCSC table browser. …

r-genenet 1.2.13

This package analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer…

r-geneplotter 1.64.0

This package provides functions for plotting genomic data. …

r-generics 0.0.2

In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics that are not provided by base R methods related to model fitting. …

r-genetics 1.3.8.1.2

This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include…

r-genie3 1.8.0

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data. …

r-genomation 1.18.0

This package provides a package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic…

r-genomationdata 1.14.0

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode. …

r-genomegraphs 1.46.0

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript…

r-genomeinfodb 1.22.0

This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural,…

r-genomeinfodbdata 1.2.0

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package. …

r-genomicalignments 1.22.1

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and…

r-genomicfeatures 1.38.1

This package provides a set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons…

r-genomicfiles 1.22.0

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation. …

r-genomicinteractions 1.20.0

This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics. …

r-genomicranges 1.38.0

This package provides tools to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The…

r-genomicscores 1.10.0

This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor. …

r-geometry 0.4.5

This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations,…

r-geoquery 2.54.1

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor…

r-geosphere 1.5-10

This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations. …

r-getopt 1.20.3

This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages `optparse' or `argparse' which…

r-getoptlong 0.1.8

This is yet another command-line argument parser which wraps the powerful Perl module `Getopt::Long' and with some adaptation for easier use in R. It also provides a simple way for variable…

r-ggally 1.4.0

The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data.…

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 1.34.0

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 1.14.0

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 0.1-20

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 0.14.0

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 0.3.1

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. Thi package aims to…

r-ggformula 0.9.2

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 0.4.8

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-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-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-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 3.2.1

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 0.0.4

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-ggpubr 0.2.4

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 2.0.0

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 0.8.1

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 0.5.2

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 0.6.0

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 0.3.3

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-ggthemes 4.2.0

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-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 0.26.1

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

r-gkmsvm 0.79.0

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 1.14.0

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 0.2.3

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 3.0-2

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 0.1.1

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 1.3.1

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 0.5-13.6

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-gofuncr 1.6.0

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 2.12.0

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 1.38.0

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 2.52.0

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 0.2.1

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-gplots 3.0.1.2

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-gqtlbase 1.18.0

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 1.18.0

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 1.64.0

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

r-graphite 1.32.0

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 0.5.0

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 0.4-1

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-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 1.20.0

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

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 1.48.0

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 3.8.1

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 1.18.0

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-gviz 1.30.1

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 2.18.0

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 1.7.9

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…

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