Packages — R (Page 5 of 25)

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r-dummies 1.5.6

This package lets you expand factors, characters and other eligible classes into dummy/indicator variables. …

r-dvmisc 1.1.4

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…

r-dyn 0.2-9.6

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…

r-dynamictreecut 1.63-1

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

r-e1071 1.7-3

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-ebarrays 2.50.0

EBarrays provides tools for the analysis of replicated/unreplicated microarray data. …

r-ebimage 4.28.1

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows…

r-ebseq 1.26.0

This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data …

r-edaseq 2.20.0

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…

r-edger 3.28.0

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…

r-effectsize 0.1.1

This package provides utilities to work with indices of effect size and standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds,…

r-egg 0.4.5

This package provides miscellaneous functions to help customize ggplot2 objects. High-level functions are provided to post-process ggplot2 layouts and allow alignment between plot panels, as well as setting panel sizes to fixed…

r-elasticnet 1.1.1

This package provides functions for fitting the entire solution path of the Elastic-Net and also provides functions for estimating sparse Principal Components. The Lasso solution paths can be computed by the…

r-ellipse 0.4.1

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.…

r-ellipsis 0.3.0

In S3 generics, it's useful to take `...' so that methods can have additional arguments. But this flexibility comes at a cost: misspelled arguments will be silently ignored. The `ellipsis'…

r-emdbook 1.3.12

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 1.4.4

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,…

r-emojifont 0.5.3

This package enables the use of emoji and the Font Awesome glyphs in both base and ggplot2 graphics. …

r-emplik 1.0-4.3

This package provides empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. It also does regression. …

r-energy 1.7-7

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…

r-enrichplot 1.6.1

The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics. …

r-enrichr 2.1

This package provides an R interface to all Enrichr databases, a web-based tool for analyzing gene sets and returns any enrichment of common annotated biological functions. …

r-ensdb-hsapiens-v75 2.99.0

This package exposes an annotation database generated from Ensembl. …

r-ensembldb 2.10.2

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…

r-epi 2.40

This package provides functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multistate data - the Lexis…

r-erm 1.0-0

This package provides tools to fit "Rasch models" (RM), "linear logistic test models" (LLTM), "rating scale model" (RSM), "linear rating scale models" (LRSM), "partial credit models" (PCM), and "linear partial credit models"…

r-erma 1.2.0

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…

r-estimability 1.3

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

r-etm 1.0.5.1

The "empirical transition matrix" (etm) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator. …

r-europepmc 0.3

This package provides an R Client for the Europe PubMed Central RESTful Web Service (https://europepmc.org/RestfulWebService). It gives access to both metadata on life science literature and open access full texts. …

r-evaluate 0.14

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. …

r-experimenthub 1.12.0

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has…

r-expint 0.1-6

This package provides the exponential integrals `E_1(x)', `E_2(x)', `E_n(x)' and `Ei(x)', and the incomplete gamma function `G(a, x)' defined for negative values of its first argument. The package also gives easy…

r-expm 0.999-4

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

r-extradistr 1.8.11

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

r-extrafont 0.17

The extrafont package makes it easier to use fonts other than the basic PostScript fonts that R uses. Fonts that are imported into extrafont can be used with PDF or PostScript…

r-extrafontdb 1.0

This package holds the database for the `extrafont' package. …

r-extremes 2.0-11

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 1.0.6

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…

r-factominer 2.2

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…

r-fail 1.3

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

r-fansi 0.4.1

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

r-farver 2.0.3

The encoding of color can be handled in many different ways, using different color spaces. As different color spaces have different uses, efficient conversion between these representations are important. This…

r-fastcluster 1.1.25

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…

r-fastica 1.2-2

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

r-fastmap 1.0.1

This package provides a fast implementation of a key-value store. Environments are commonly used as key-value stores, but every time a new key is used, it is added to R's global…

r-fastmatch 1.1-0

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…

r-fastseg 1.32.0

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…

r-fda 2.4.8.1

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. The package includes data…

r-fdb-infiniummethylation-hg19 2.2.0

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations. …

r-fdrtool 1.2.15

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…

r-feather 0.3.5

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

r-feature 1.2.13

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

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

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

r-fftwtools 0.9-8

This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. …

r-fgsea 1.12.0

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate…

r-fgui 1.0-8

Rapidly create a GUI for a function you created by automatically creating widgets for arguments of the function. This package automatically parses help routines for context-sensitive help to these arguments. …

r-fields 10.3

This is a package for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and…

r-filematrix 1.3

This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes…

r-findpython 1.0.5

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

r-fit-models 0.5-14

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…

r-fitdistrplus 1.0-14

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,…

r-fithic 1.12.0

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

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

r-flare 1.6.0.2

This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models. …

r-flashclust 1.01-2

This package provides a fast implementation of hierarchical clustering. …

r-flexclust 1.4-0

The main function `kcca' implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There…

r-flexdashboard 0.5.1.1

This package provides an R Markdown format for converting an R Markdown document to a grid-oriented dashboard. The dashboard flexibly adapts the size of its components to the containing web page. …

r-flexmix 2.3-15

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…

r-flextable 0.5.8

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…

r-flock 0.7

This package implements synchronization between R processes (spawned by using the `parallel' package for instance) using file locks. It supports both exclusive and shared locking. …

r-flowclust 3.24.0

This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation. …

r-flowcore 1.52.1

This package provides S4 data structures and basic functions to deal with flow cytometry data. …

r-flowmeans 1.46.0

This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. …

r-flowsom 1.18.0

FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees. …

r-flowstats 3.44.0

This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the `flowCore' package. …

r-flowutils 1.50.0

This package provides utilities for flow cytometry data. …

r-flowviz 1.50.0

This package provides visualization tools for flow cytometry data. …

r-flowworkspace 3.34.1

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the…

r-fmsb 0.7.0

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…

r-fnn 1.1.3

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 0.4.0

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…

r-foreach 1.4.8

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. …

r-forecast 8.11

This package provides methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling. …

r-foreign 0.8-75

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 1.7

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…

r-formula 1.2-3

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…

r-fpc 2.2-5

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…

r-fracdiff 1.5-1

This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods. …

r-fractal 2.0-4

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

r-fs 1.3.1

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

r-furrr 0.1.0

This package provides implementations of the family of `map()' functions from the `purrr' package that can be resolved using any `future'-supported backend, e.g. parallel on the local machine or distributed on…

r-futile-logger 1.4.3

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'…

r-futile-options 1.0.1

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…

r-future 1.16.0

The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. This package implements sequential, multicore, multisession, and…

r-future-apply 1.4.0

This package provides implementations of `apply()', `eapply()', `lapply()', `Map()', `mapply()', `replicate()', `sapply()', `tapply()', and `vapply()' that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on…

r-gage 2.36.0

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…

r-gamlss 5.1-6

This package provides functions for fitting the generalized additive models for location scale and shape introduced by Rigby and Stasinopoulos (2005), `doi:10.1111/j.1467-9876.2005.00510.x'. The models use a distributional regression approach where all the…

r-gamlss-data 5.1-4

This package provides data used as examples to demonstrate GAMLSS models. …

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