Packages — R (Page 3 of 11)

r-drr 0.0.3 — Dimensionality reduction via regression

This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.

r-dt 0.5 — R wrapper of the DataTables JavaScript library

This package allows for data objects in R to be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package.

r-dtw 1.20-1 — Dynamic Time Warping Algorithms

This package provides a comprehensive implementation of dynamic time warping (DTW) algorithms in R. DTW computes the optimal (least cumulative distance) alignment between points of two time series. Common DTW variants covered include local (slope) and global (window) constraints, subsequence matches, arbitrary distance definitions, normalizations, minimum variance matching, and so on.

r-dvmisc 1.1.2 — Faster computation of common statistics and miscellaneous functions

This package implements faster versions of base R functions (e.g. mean, standard deviation, covariance, weighted mean), mostly written in C++, along with miscellaneous functions for various purposes (e.g. create the histogram with fitted probability density function or probability mass function curve, create the body mass index groups, assess the linearity assumption in logistic regression).

r-dyn 0.2-9.6 — Time series regression

This package provides the dyn class interfaces ts, irts, zoo and zooreg time series classes to lm, glm, loess, quantreg::rq, MASS::rlm, MCMCpack::MCMCregress(), quantreg::rq(), randomForest::randomForest() and other regression functions, allowing those functions to be used with time series including specifications that may contain lags, diffs and missing values.

r-dynamictreecut 1.63-1 — Detect clusters in hierarchical clustering dendrograms

This package contains methods for the detection of clusters in hierarchical clustering dendrograms.

r-e1071 1.7-0 — Miscellaneous functions for probability theory

This package provides functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, and more.

r-edaseq 2.16.0 — Exploratory data analysis and normalization for RNA-Seq

This package provides support for numerical and graphical summaries of RNA-Seq genomic read data. Provided within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization. Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization.

r-edger 3.24.0 — EdgeR does empirical analysis of digital gene expression data

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

r-ellipse 0.4.1 — Functions for drawing ellipses and ellipse-like confidence regions

This package contains various routines for drawing ellipses and ellipse-like confidence regions, implementing the plots described in Murdoch and Chow (1996), A graphical display of large correlation matrices, The American Statistician 50, 178-180. There are also routines implementing the profile plots described in Bates and Watts (1988), Nonlinear Regression Analysis and its Applications.

r-emdbook 1.3.10 — Support functions and data for "Ecological Models and Data"

This package provides auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

r-emmeans 1.3.0 — Estimated marginal means, aka least-squares means

This package provides tools to obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. It can be used to compute contrasts or linear functions of EMMs, trends, and comparisons of slopes.

r-energy 1.7-5 — Multivariate inference via the energy of data

This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.

r-ensembldb 2.6.2 — Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript-centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package also provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

r-erma 0.14.0 — Epigenomic road map adventures

The epigenomics road map describes locations of epigenetic marks in DNA from a variety of cell types. Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin. This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.

r-estimability 1.3 — Tools for assessing estimability of linear predictions

Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly.

r-evaluate 0.12 — Parsing and evaluation tools for R

This package provides tools that allow you to recreate the parsing, evaluation and display of R code, with enough information that you can accurately recreate what happens at the command line. The tools can easily be adapted for other output formats, such as HTML or LaTeX.

r-expm 0.999-3 — Tools for matrix exponentials and related quantities

This package provides tools for the computation of the matrix exponential, logarithm, square root, and related quantities.

r-extradistr 1.8.10 — Additional univariate and multivariate distributions

This package implements density, distribution functions, quantile functions and random generation functions for a large number of univariate and multivariate distributions.

r-extremes 2.0-9 — Extreme value analysis

ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.

r-factoextra 1.0.5 — Extract and visualize the results of multivariate data analyses

This package provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including PCA (Principal Component Analysis), CA (Correspondence Analysis), MCA (Multiple Correspondence Analysis), FAMD (Factor Analysis of Mixed Data), MFA (Multiple Factor Analysis) and HMFA (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides ggplot2-based elegant data visualization.

r-factominer 1.41 — Multivariate exploratory data analysis and data mining

This package provides exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.

r-fail 1.3 — File abstraction interface layer (FAIL)

This package provides a more comfortable interface to work with R data or source files in a key-value fashion.

r-fansi 0.4.0 — ANSI control sequence aware string functions

This package provides counterparts to R string manipulation functions that account for the effects of ANSI text formatting control sequences.

r-fastcluster 1.1.25 — Fast hierarchical clustering routines

This package implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package scipy.cluster.hierarchy, hclust() in R's stats package, and the flashClust package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.

r-fastica 1.2-1 — FastICA algorithms to perform ICA and projection pursuit

This package provides an implementation of the FastICA algorithm to perform independent component analysis (ICA) and projection pursuit.

r-fastmatch 1.1-0 — Fast match function

This package provides a fast match replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.

r-fastseg 1.28.0 — Fast segmentation algorithm for genetic sequencing data

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

r-fdrtool 1.2.15 — Estimation of false discovery rates and higher criticism

This package provides tools to estimate tail area-based false discovery rates as well as local false discovery rates for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.

r-feather 0.3.1 — R Bindings to the Feather API

Read and write feather files, a lightweight binary columnar daa store designed for maximum speed.

r-feature 1.2.13 — Inferential feature significance for kernel density estimation

The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes).

r-ff 2.2-14 — Memory-efficient storage of large data on disk and access functions

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

r-ffbase 0.12.7 — Basic statistical functions for package 'ff'

This package extends the out of memory vectors of ff with statistical functions and other utilities to ease their usage.

r-findpython 1.0.3 — Functions to find an acceptable Python binary

This package was designed to find an acceptable Python binary that matches version and feature constraints.

r-fit-models 0.5-14 — Compare fitted models

The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to compare robustly and classically fitted model objects. The aim of the fit.models package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.

r-fitdistrplus 1.0-11 — Fitting a parametric distribution from data

This package extends the fitdistr function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.

r-fithic 1.8.0 — Confidence estimation for intra-chromosomal contact maps

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

r-fivethirtyeight 0.1.0 — Data and code behind the stories at FiveThirtyEight

This R package provides access to the code and data sets published by the statistics blog FiveThirtyEight.

r-flashclust 1.01-2 — Implementation of optimal hierarchical clustering

This package provides a fast implementation of hierarchical clustering.

r-flexmix 2.3-14 — Flexible mixture modeling

This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.

r-flextable 0.4.6 — Functions for tabular reporting

This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the officer package and can be used within R markdown documents when rendering to HTML and to Word documents.

r-fmsb 0.6.3 — Functions for medical statistics book with demographic data

This package provides several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.

r-fnn — Fast nearest neighbor search algorithms and applications

This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented.

r-forcats 0.3.0 — Tools for working with factors

This package provides helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into other, "anonymizing", and manually "recoding").

r-foreach 1.4.4 — Foreach looping construct for R

This package provides support for the foreach looping construct. foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

r-foreign 0.8-71 — Read data stored by other statistics software

This package provides functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.

r-formatr 1.5 — Format R code automatically

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

r-formula 1.2-3 — Extended model formulas

This package provides a new class Formula, which extends the base class formula. It supports extended formulas with multiple parts of regressors on the right-hand side and/or multiple responses on the left-hand side.

r-fpc 2.1-11.1 — Flexible procedures for clustering

This package provides various methods for clustering and cluster validation. For example, it provides fixed point clustering, linear regression clustering, clustering by merging Gaussian mixture components, as well as symmetric and asymmetric discriminant projections for visualisation of the separation of groupings.

r-fractal 2.0-4 — Fractal time series modeling and analysis

This package provides tools for stochastic fractal and deterministic chaotic time series analysis.

r-fs 1.2.6 — Cross-platform file system operations based on libuv

This package provides a cross-platform interface to file system operations, built on top of the libuv C library.

r-futile-logger 1.4.3 — Logging utility for R

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

r-futile-options 1.0.1 — Options management framework

The futile.options subsystem provides an easy user-defined options management system that is properly scoped. This means that options created via futile.options are fully self-contained and will not collide with options defined in other packages.

r-gage 2.32.0 — Generally applicable gene-set enrichment for pathway analysis

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. The gage package provides functions for basic GAGE analysis, result processing and presentation. In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.

r-gbrd 0.4-11 — Utilities for processing Rd objects and files

This package provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions.

r-gclus 1.3.1 — Clustering graphics

This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of pairs and parcoord which color panels according to their merit level.

r-gdata 2.18.0 — Various R programming tools for data manipulation

This package provides various R programming tools for data manipulation, including:

  • medical unit conversions

  • combining objects

  • character vector operations

  • factor manipulation

  • obtaining information about R objects

  • manipulating MS-Excel formatted files

  • generating fixed-width format files

  • extricating components of date and time objects

  • operations on columns of data frames

  • matrix operations

  • operations on vectors and data frames

  • value of last evaluated expression

  • wrapper for sample that ensures consistent behavior for both scalar and vector arguments

r-gdtools 0.1.7 — Utilities for graphical rendering

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

r-genefilter 1.64.0 — Filter genes from high-throughput experiments

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

r-genelendatabase 1.16.0 — Lengths of mRNA transcripts for a number of genomes

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-geneplotter 1.60.0 — Graphics functions for genomic data

This package provides functions for plotting genomic data.

r-genomation 1.14.0 — Summary, annotation and visualization of genomic data

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 intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.

r-genomationdata 1.14.0 — Experimental data for use with the genomation package

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

r-genomeinfodb 1.18.1 — Utilities for manipulating chromosome identifiers

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, rather than lexicographic, order.

r-genomeinfodbdata 1.2.0 — Species and taxonomy ID look up tables for GenomeInfoDb

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

r-genomicalignments 1.18.0 — Representation and manipulation of short genomic alignments

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 working with the nucleotide content of the alignments.

r-genomicfeatures 1.34.1 — Tools for working with transcript centric annotations

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 and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

r-genomicfiles 1.18.0 — Distributed computing by file or by range

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 1.16.0 — R package for handling genomic interaction data

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 1.34.0 — Representation and manipulation of genomic intervals

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 GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.

r-geometry 0.3-6 — Mesh generation and surface tesselation

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, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the Quickhull algorithm for computing the convex hull. Qhull does not support constrained Delaunay triangulations, or mesh generation of non-convex objects, but the package does include some R functions that allow for this. Currently the package only gives access to Delaunay triangulation and convex hull computation.

r-geosphere 1.5-7 — Spherical trigonometry

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

r-getopt 1.20.2 — Command-line option processor for R

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 add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.

r-getoptlong 0.1.7 — Parsing command-line arguments and variable interpolation

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 interpolation in R.

r-ggally 1.4.0 — Extension to ggplot2

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. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.

r-ggbeeswarm 0.6.0 — Categorical scatter (violin point) plots

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 1.30.0 — Visualization tools for genomic data

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 data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

r-ggdendro 0.1-20 — Create Dendrograms and Tree Diagrams Using ggplot2

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 directly to a plot device with out exposing the data. The ggdendro package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.

r-ggeffects 0.7.0 — Create tidy data frames of marginal effects for ggplot

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. Marginal effects can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The two main functions are ggpredict() and ggeffect(). There is a generic plot() method to plot the results using ggplot2.

r-ggformula 0.9.0 — Formula interface for the r-ggplot2

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 providing the intuitive capabilities of r-ggplot2.

r-ggjoy 0.4.1 — Joyplots in ggplot2

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 2.6.1 — Spatial visualization with ggplot2

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 common to those tasks, including functions for geolocation and routing.

r-ggplot2 3.1.0 — An implementation of the grammar of graphics

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 still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes.

r-ggpubr 0.2 — ggplot2-based publication-ready plots

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. The ggpubr package provides some easy-to-use functions for creating and customizing ggplot2-based publication-ready plots.

r-ggrepel 0.8.0 — Repulsive text and label geometries for ggplot2

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 0.5.1 — Ridgeline plots in ggplot2

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 — Scientific journal and sci-fi themed color palettes for ggplot2

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 — ggplot2 extension for drawing genetic sequence logos

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 to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other ggplot2 plots.

r-ggsignif 0.4.0 — Significance brackets for ggplot2

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 the groups of interest which itself is annotated with the level of significance. The package provides a single layer that takes the groups for comparison and the test as arguments and adds the annotation to the plot.

r-ggstance 0.3.1 — Horizontal and vertical versions of r-ggplot2

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 4.0.1 — Extra themes, scales and geoms for ggplot2

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, among others. This package also provides geoms for Tufte's box plot and range frame.

r-gh 1.0.1 — Access the GitHub API via R

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

r-git2r 0.23.0 — Access Git repositories with R

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 — Gapped-kmer support vector machine

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-glimma 1.10.0 — Interactive HTML graphics

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 static representations of analysis results in order to provide additional information.

r-glmmtmb — Generalized linear mixed models

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 be Gaussian on the scale of the linear predictor and are integrated out using the Laplace approximation. Gradients are calculated using automatic differentiation.

r-glmnet 2.0-16 — Lasso and elastic-net regularized generalized linear models

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. The algorithm uses cyclical coordinate descent in a path-wise fashion.

r-globaloptions 0.1.0 — Generate functions to get or set global options

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

r-glue 1.3.0 — Interpreted string literals

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-go-db 3.7.0 — Annotation maps describing the entire Gene Ontology

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