Packages — R (Page 6 of 58)

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### r-delaporte 8.0.2

This package provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution with parameterization based on Vose (2008). The Delaporte is a discrete probability distribution which can…

### r-delayedarray 0.20.0

Wrapping an array-like object (typically an on-disk object) in a `DelayedArray' object allows one to perform common array operations on it without loading the object in memory. In order to reduce…

### r-delayedmatrixstats 1.16.0

This package provides a port of the `matrixStats' API for use with `DelayedMatrix' objects from the `DelayedArray' package. It contains high-performing functions operating on rows and columns of `DelayedMatrix' objects, e.g. …

### r-deldir 1.0-6

This package provides tools for calculating the Delaunay triangulation and the Dirichlet or Voronoi tessellation (with respect to the entire plane) of a planar point set. It plots triangulations and tessellations…

### r-demultiplex 1.0.2-1.6e2a142

deMULTIplex is an R package for analyzing single-cell RNA sequencing data generated with the MULTI-seq sample multiplexing method. The package includes software to 1. Convert raw MULTI-seq sample barcode library…

### r-dendextend 1.15.2

This package offers a set of functions for extending `dendrogram' objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color,…

### r-densestbayes 1.0-2.1

Bayesian density estimates for univariate continuous random samples are provided using the Bayesian inference engine paradigm. The engine options are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field variational Bayes…

### r-densityclust 0.3.2

This package provides an improved implementation (based on k-nearest neighbors) of the density peak clustering algorithm, originally described by Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can…

### r-deoptimr 1.0-11

This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1)…

### r-depecher 1.10.0

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of…

### r-depmixs4 1.5-0

This package fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models. …

### r-depth 2.1-1.1

This package provides tools for depth functions methodology applied to multivariate analysis. Besides allowing calculation of depth values and depth-based location estimators, the package includes functions or drawing contour plots and perspective…

### r-derfinderhelper 1.28.0

This package speeds up the derfinder package when using multiple cores. It is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when…

### r-deriv 4.1.3

This package provides an R-based solution for symbolic differentiation. It admits user-defined functions as well as function substitution in arguments of functions to be differentiated. Some symbolic simplification is part…

### r-desc 1.4.1

This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages. …

### r-desctools 0.99.44

This package provides a collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first…

### r-deseq 1.39.0

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution. …

### r-deseq2 1.34.0

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution. …

### r-desolve 1.31

This package provides functions that solve initial value problems of a system of first-order "ordinary differential equations" (ODE), of "partial differential equations" (PDE), of "differential algebraic equations" (DAE), and of delay differential equations.…

### r-destiny 3.8.1

This package provides tools to create and plot diffusion maps. …

### r-devtools 2.4.3

The devtools package is a collection of package development tools to simplify the devolpment of R packages. …

### r-dexseq 1.40.0

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical…

### r-diagram 1.6.5

This package provides tools to visualize simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams, visualizing webs, electrical networks, etc. It also includes supporting material for the…

### r-dials 0.1.1

Many models contain tuning parameters (i.e. parameters that cannot be directly estimated from the data). These tools can be used to define objects for creating, simulating, or validating values for…

### r-dicedesign 1.9

This package provides tools to create some specific `Space-Filling Design' (SFD) and to test their quality. …

### r-dichromat 2.0-0

Dichromat collapses red-green or green-blue distinctions to simulate the effects of different types of color-blindness. …

### r-diffbind 3.4.11

This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. …

### r-diffcyt 1.14.0

This package provides statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes…

### r-diffobj 0.3.5

Generate a colorized diff of two R objects for an intuitive visualization of their differences. …

### r-diffusionmap 1.2.0

This package implements the diffusion map method of data parametrization, including creation and visualization of diffusion maps, clustering with diffusion K-means and regression using the adaptive regression model. …

### r-digest 0.6.29

This package contains an implementation of a function `digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison…

### r-dimred 0.2.5

This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods. …

### r-diptest 0.76-0

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected. …

### r-dir-expiry 1.2.0

This package implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims…

### r-directlabels 2021.1.13

This package provides an extensible framework for automatically placing direct labels onto multicolor plots. Label positions are described using positioning methods that can be re-used across several different plots. There…

### r-dirichletmultinomial 1.36.0

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE…

### r-dirichletreg 0.7-1

This package implements Dirichlet regression models. …

### r-dismo 1.3-5

This package provides methods for species distribution modeling, i.e., predicting the environmental similarity of any site to that of the locations of known occurrences of a species. …

### r-distillery 1.2-1

This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx. …

### r-distributional 0.3.0

This package provides vectorized distribution objects with tools for manipulating, visualizing, and using probability distributions. It was designed to allow model prediction outputs to return distributions rather than their parameters, allowing users…

### r-distributionutils 0.6-0

This package provides utilities for dealing with distributions. Functionality includes sample skewness and kurtosis, log-histogram, tail plots, moments by integration, changing the point about which a moment is calculated, functions for testing…

### r-diversitree 0.9-16

This package contains a number of comparative "phylogenetic" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of "BiSSE" (Binary State Speciation and Extinction) and its unresolved tree extensions, "MuSSE"…

### r-dlm 1.1-5

This package provides routines for Maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Normal linear State Space models, also known as Dynamic Linear Models. …

### r-dlmap 1.13

This is package for QTL mapping in a mixed model framework with separate detection and localization stages. The first stage detects the number of QTL on each chromosome based on the…

### r-dmrseq 1.14.0

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing…

### r-dnabarcodes 1.24.0

This package offers tools to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally,…

### r-dnacopy 1.68.0

This package implements the "circular binary segmentation" (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number. …

### r-do-db 2.9

This package provides a set of annotation maps describing the entire Disease Ontology. …

### r-doby 4.6.12

This package contains: * facilities for working with grouped data: `do' something to data stratified `by' some variables. * implementations of least-squares…

### r-docopt 0.7.1

This package enables you to define a command-line interface by just giving it a description in the specific format. …

### r-dofuture 0.12.1

This package provides a `%dopar%' adapter such that any type of futures can be used as backends for the `foreach' framework. …

### r-domc 1.3.8

This package provides a parallel backend for the `%dopar%' function using the multicore functionality of the parallel package. …

### r-doparallel 1.0.17

This package provides a parallel backend for the `%dopar%' function using the parallel package. …

### r-dorng 1.8.2

This package provides functions to perform reproducible parallel `foreach' loops, using independent random streams as generated by L'Ecuyer's combined multiple-recursive generator. It enables to easily convert standard `%dopar%' loops into fully reproducible…

### r-dose 3.20.1

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang, respectively, for measuring semantic similarities among "Disease ontology" (DO) terms and gene products. Enrichment analyses including hypergeometric model and…

### r-dosnow 1.0.20

This package provides a parallel backend for the `%dopar%' function using the `snow' package. …

### r-dot 0.1

This package provides tools to render DOT diagram markup language in R and also provides the possibility to export the graphs in PostScript and SVG (Scalable Vector Graphics) formats. In addition,…

### r-dotcall64 1.0-1

This package provides `.C64()', an enhanced version of `.C()' and `.Fortran()' from the R foreign function interface. `.C64()' supports long vectors, arguments of type 64-bit integer, and provides a mechanism to…

### r-doubletfinder 2.0.3-1.554097b

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for…

### r-downlit 0.4.0

This package provides syntax highlighting of R code, specifically designed for the needs of RMarkdown packages like `pkgdown', `hugodown', and `bookdown'. It includes linking of function calls to their documentation on…

### r-downloader 0.4

This package provides a wrapper for the `download.file' function, making it possible to download files over HTTPS across platforms. The `RCurl' package provides this functionality (and much more) but has external…

### r-dplyr 1.0.8

dplyr is the next iteration of plyr. It is focused on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools…

### r-dqrng 0.3.0

Several fast random number generators are provided as C++ header-only libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+. Additionally, fast functions for generating random numbers according to a uniform,…

### r-drc 3.0-1

This package provides a suite of flexible and versatile model fitting and after-fitting functions for the analysis of dose-response data. …

### r-drimpute 1.0

This is an R package for imputing dropout events. Many statistical methods in cell type identification, visualization and lineage reconstruction do not account for dropout events. DrImpute can improve the…

### r-drimseq 1.22.0

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic…

### r-dropbead 0-2.d746c6f

This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq. …

### r-drr 0.0.4

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

### r-drtmle 1.1.0

This package implements targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality. …

### r-dt 0.22

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…

### r-dtplyr 1.2.1

This package provides a `data.table' backend for `dplyr'. The goal of `dtplyr' is to allow you to write `dplyr' code that is automatically translated to the equivalent, but usually much faster,…

### r-dtt 0.1-2

This package provides functions for 1D and 2D Discrete Cosine Transform ("DCT"), Discrete Sine Transform ("DST") and Discrete Hartley Transform ("DHT"). …

### r-dtw 1.22-3

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…

### 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-dygraphs 1.1.1.6

This package provides an R interface to the dygraphs JavaScript charting library (a copy of which is included in the package). It provides rich facilities for charting time-series data in R,…

### 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-dyngen 1.0.3-1.37fd179

This package provides a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. …

### r-dynutils 1.0.9

This package provides common functionality for the dynverse (https://dynverse.org) packages. dynverse is created to support the development, execution, and benchmarking of trajectory inference methods. …

### r-e1071 1.7-9

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 2.58.0

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

### r-ebimage 4.36.0

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 1.34.0

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

### r-ecp 3.1.3

This package implements various procedures for finding multiple change-points. Two methods make use of dynamic programming and pruning, with no distributional assumptions other than the existence of certain absolute moments in one…

### r-edaseq 2.28.0

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 3.36.0

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-effects 4.2-1

Graphical and tabular effect displays, e.g., of interactions, for various statistical models with linear predictors. …

### r-effectsize 0.6.0.1

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 1.3

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 0.4.2

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 0.3.2

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-elliptic 1.4-0

A suite of elliptic and related functions including Weierstrass and Jacobi forms. Also includes various tools for manipulating and visualizing complex functions. …

### 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-emdist 0.3-2

This package provides tools to calculate the Earth Mover's Distance (EMD). …

### r-emmeans 1.7.3

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 0.5.5

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

### r-emplik 1.1-1

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

### r-energy 1.7-9

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…