Packages — R (Page 6 of 61)

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r-cytonorm 0.0.7-1.e4b9d34

This package can be used to normalize cytometry samples when a control sample is taken along in each of the batches. This is done by first identifying multiple clusters/cell types, learning…

r-d3network 0.5.2.1

This package is intended to make it easy to create D3 JavaScript network, tree, dendrogram, and Sankey graphs from R using data frames. …

r-d3r 1.0.0

This package provides a suite of functions to help ease the use of the d3.js visualization library in R. These helpers include `htmltools::htmlDependency' functions, hierarchy builders, and conversion tools for `partykit',…

r-dae 3.2-13

This package provides functions useful in the design and ANOVA of experiments. The content falls into the following groupings: 1. data, 2. factor manipulation functions, 3. design functions, …

r-dalex 2.4.2

Machine Learning models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance,…

r-data-table 1.14.2

The R package `data.table' is an extension of `data.frame' providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column…

r-data-tree 1.0.0

Create tree structures from hierarchical data, and traverse the tree in various orders. Aggregate, cumulate, print, plot, convert to and from data.frame and more. This is useful for decision trees,…

r-datasaurus 0.1.6

The Datasaurus Dozen is a set of datasets with the same summary statistics. They retain the same summary statistics despite having radically different distributions. The datasets represent a larger and…

r-datawizard 0.6.0

This package provides a lightweight package to easily manipulate, clean, transform, and prepare your data for analysis. It also forms the data wrangling backend for the packages in the `easystats' ecosystem. …

r-dbi 1.1.3

The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by…

r-dbplyr 2.2.1

This package provides a dplyr back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database…

r-dbscan 1.1-10

This package provides a fast reimplementation of several density-based algorithms of the DBSCAN family. It includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and "hierarchical DBSCAN" (HDBSCAN), the…

r-dcv 0.1.1

This package performs several conventional cross-validation statistical methods for climate-growth model in the climate reconstruction from tree rings, including Sign Test statistic, Reduction of Error statistic, Product Mean Test, Durbin-Watson statistic etc. …

r-ddalpha 1.3.13

This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function…

r-ddrtree 0.1.5

This package provides an implementation of the framework of "reversed graph embedding" (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of…

r-dearseq 1.8.4

This is a package for Differential Expression Analysis of RNA-seq data. It features a variance component score test accounting for data heteroscedasticity through precision weights. Perform both gene-wise and gene…

r-debugme 1.1.0

This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables. …

r-decipher 2.24.0

This package provides a toolset for deciphering and managing biological sequences. …

r-decon 1.3-4

This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement…

r-deconstructsigs 1.8.0

This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely…

r-deconvr 1.2.0

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the…

r-decoupler 2.2.2

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. decoupleR is a Bioconductor package…

r-deds 1.60.0

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also…

r-deepsnv 1.42.1

This package provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the…

r-delaporte 8.0.3

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 0.22.0

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 1.18.1

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 1.16.0

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 1.12.0

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 1.30.0

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 1.4.2

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 0.99.46

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 1.36.0

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 1.33

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 3.10.0

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

r-devtools 2.4.4

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

r-dexseq 1.42.0

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 1.0.0

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 2.0-0.1

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

r-diffbind 3.6.4

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 1.16.0

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 0.2.6

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 1.4.0

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 1.38.0

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 1.3-8

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 0.3.1

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-dittoseq 1.8.1

This package provides a universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat…

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-dixontest 1.0.4

For outlier detection in small and normally distributed samples the ratio test of Dixon (Q-test) can be used. Density, distribution function, quantile function and random generation for Dixon's ratio statistics are…

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 1.16.0

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 1.26.0

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 1.70.0

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 4.6.13

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 0.12.2

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 3.22.1

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 0.4.2

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 1.0.10

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 1.24.0

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 1.1.1

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 0.25

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 1.2.2

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. …

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