Packages — R (Page 5 of 51)

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r-commonmark 1.7

The CommonMark specification defines a rationalized version of markdown syntax. This package uses the `cmark' reference implementation for converting markdown text into various formats including HTML, LaTeX and groff man. In…

r-compare 0.2-6

This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects…

r-complexheatmap 2.8.0

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation…

r-complexplus 2.1

This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant. …

r-compositions 2.0-2

This package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations). …

r-compquadform 1.4.3

This package provides functions to compute the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm. …

r-config 0.3.1

This package lets you manage configuration values across multiple environments (e.g. development, test, production). It reads values using a function that determines the current environment and returns the appropriate value. …

r-conflicted 1.0.4

R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that…

r-conquer 1.0.2

This package provides fast and accurate convolution-type smoothed quantile regression, implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Confidence intervals for regression coefficients are constructed using multiplier bootstrap. …

r-consensusclusterplus 1.56.0

This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis. …

r-contfrac 1.1-12

Various utilities for evaluating continued fractions. …

r-copyhelper 1.6.0

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38,…

r-copynumber 1.32.0

This package segments single- and multi-track copy number data by a penalized least squares regression method. …

r-copywriter 2.24.0

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied…

r-corpcor 1.6.10

This package implements a James-Stein-type shrinkage estimator for the covariance matrix, with separate shrinkage for variances and correlations. Furthermore, functions are available for fast singular value decomposition, for computing the pseudoinverse, and for…

r-corrplot 0.90

This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including…

r-coverageview 1.30.0

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or…

r-covr 3.5.1

Thisp package enables you to track and report code coverage for your package and (optionally) upload the results to a coverage service. Code coverage is a measure of the amount of…

r-cowplot 1.1.1

This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications. …

r-cpp11 0.4.0

This package provides a header only, C++11 interface to R's C interface. Compared to other approaches `cpp11' strives to be safe against long jumps from the C API as well as C++…

r-crayon 1.4.1

Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be…

r-credentials 1.3.1

This package assists you in setting up and retrieving of HTTPS and SSH credentials for use with git and other services. For HTTPS remotes the package interfaces the `git-credential' utility which…

r-crochet 2.3.0

Functions to help implement the extraction / subsetting / indexing function `[' and replacement function `[<-' of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix…

r-crosstalk 1.1.1

This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static `.html' files). It currently supports linked brushing and filtering. …

r-crul 1.1.0

This package provides a simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's `faraday' gem. …

r-cssam 1.4-1.9ec58c9

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM. …

r-ctc 1.66.0

This package provides tools for exporting and importing classification trees and clusters to other programs. …

r-cubature 2.0.4.2

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both `hcubature' and `pcubature' routines in addition to a vector interface. …

r-cummerbund 2.34.0

This package allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. …

r-curatedtcgadata 1.8.0

This package provides publicly available data from The Cancer Genome Atlas (TCGA) as `MultiAssayExperiment' objects. `MultiAssayExperiment' integrates multiple assays (e.g., RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological…

r-curl 4.3.2

The `curl()' and `curl_download()' functions provide highly configurable drop-in replacements for base `url()' and `download.file()' with better performance, support for encryption, gzip compression, authentication, and other `libcurl' goodies. The core of the…

r-curry 0.1.1

Partial application is the process of reducing the arity of a function by fixing one or more arguments, thus creating a new function lacking the fixed arguments. The `curry' package provides three…

r-cvauc 1.1.0

This package contains various tools for working with and evaluating cross-validated area under the ROC curve (AUC) estimators. The primary functions of the package are `ci.cvAUC' and `ci.pooled.cvAUC', which report cross-validated AUC…

r-cvst 0.2-2

This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on…

r-cyclocomp 1.1.0

Cyclomatic complexity is a software metric, used to indicate the complexity of a program. It is a quantitative measure of the number of linearly independent paths through a program's source code.…

r-cytolib 2.4.0

This package provides the core data structure and API to represent and interact with gated cytometry data. …

r-cytoml 2.4.0

This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms. …

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 3.2-11

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 2.3.0

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 1.14.0

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 0.1.4

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 0.2.0.1

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 1.1.1

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 2.1.1

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-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 1.3.11

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-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 2.20.0

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

r-decon 1.2-4

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-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 1.38.0

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 8.0.1

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 0.18.0

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 1.14.3

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 0.2-10

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 1.15.1

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-densityclust 0.3

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 1.0-9

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 1.8.0

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-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 1.3.0

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

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 1.32.0

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 1.29

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 2.4.2

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

r-dexseq 1.38.0

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 0.0.10

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 3.2.7

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 0.3.4

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 0.6.28

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 0.76-0

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 1.0.0

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 1.34.0

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-dismo 1.3-3

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 0.2.2

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-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 1.12.0

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 1.22.0

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 1.66.0

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 4.6.11

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

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