Packages — R (Page 5 of 39)

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### r-deseq2 1.30.0

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 1.28

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 3.4.0

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

### r-devtools 2.3.2

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

### r-dexseq 1.36.0

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 0.0.9

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 1.8-1

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 3.0.8

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

### r-diffobj 0.3.2

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 0.6.27

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 0.2.3

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

### r-diptest 0.75-7

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-directlabels 2020.6.17

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 1.32.0

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-distillery 1.2

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-diversitree 0.9-15

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-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-dnabarcodes 1.20.0

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 1.64.0

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 4.6.8

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-domc 1.3.7

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

### r-doparallel 1.0.16

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 3.16.0

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 1.0.19

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 1.0-0

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-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 1.0.2

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

### r-dqrng 0.2.1

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-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-dt 0.16

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-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-e1071 1.7-4

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 2.54.0

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

### r-ebimage 4.32.0

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 1.30.0

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 2.24.0

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 3.32.0

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 0.4.1

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 0.3.1

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 1.5.2-1

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 1.1-1

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

### r-energy 1.7-7

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 1.10.1

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 2.14.0

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-entropy 1.2.1

This package implements various estimators of entropy, such as the shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen estimator. It…

### r-epi 2.42

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 1.0-1

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 1.6.0

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 1.1.1

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

### r-etrunct 0.1

This package computes moments of univariate truncated T distribution. There is only one exported function, `e_trunct', which should be seen for details. …

### r-europepmc 0.4

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-exactranktests 0.8-31

This package computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel. …

### r-experimenthub 1.16.0

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 0.999-5

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

### r-extradistr 1.9.1

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 2.1

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 1.0.7

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 2.3

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 1.36.0

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-fastshap 0.0.5

This package computes fast (relative to other implementations) approximate Shapley values for any supervised learning model. Shapley values help to explain the predictions from any black box model using ideas from…

### r-fda 5.1.7

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-fds 1.8

This package contains a list of functional time series, sliced functional time series, and functional data sets. Functional time series is a special type of functional data observed over time. …

### r-feather 0.3.5

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