Packages — R (Page 4 of 33)

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r-chipkernels 1.1-1.c9cfcacb6

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for…

r-chippeakanno 3.22.3

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and…

r-chipseq 1.38.0

This package provides tools for processing short read data from ChIPseq experiments. …

r-chron 2.3-56

This package provides chronological R objects which can handle dates and times. …

r-cicero 1.6.2

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data. …

r-cicero-monocle3 1.3.2-1.fa2fb65

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data. …

r-circlize 0.4.10

Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. …

r-circular 0.4-93

This package provides tools for circular statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific. …

r-circus 0.1.5

Circus is an R package for annotation, analysis and visualization of circRNA data. Users can annotate their circRNA candidates with host genes, gene featrues they are spliced from, and discriminate between…

r-cistopic 0.2.1-0.29abd8d

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as "Latent Dirichlet Allocation" (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single…

r-citr 0.3.2

This package provides functions and an RStudio add-in that search a BibTeX or BibLaTeX file to create and insert formatted Markdown citations into the current document. …

r-class 7.3-17

This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps. …

r-classint 0.4-3

This package provides selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes. …

r-cli 2.0.2

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives. …

r-clipr 0.7.0

This package provides simple utility functions to read from and write to the system clipboards. …

r-clisymbols 1.2.0

This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode. …

r-clue 0.3-57

Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. This R package provides an extensible…

r-cluster 2.1.0

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding…

r-clusterprofiler 3.16.1

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters. …

r-clusterr 1.2.2

This package provides Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes…

r-clusteval 0.1

This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters. …

r-cmprsk 2.2-10

This package provides tool for estimation, testing and regression modeling of subdistribution functions in competing risks, as described in Gray (1988), A class of K-sample tests for comparing the cumulative incidence of…

r-cobs 1.3-4

This package provides qualitatively constrained (regression) smoothing splines via linear programming and sparse matrices. …

r-coda 0.19-3

This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain. …

r-codedepends 0.6.5

This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of…

r-codetools 0.2-16

This package provides code analysis tools for R to check R code for possible problems. …

r-coin 1.3-1

This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems. …

r-colorout 1.2-2

`colorout' is an R package that colorizes R output when running in terminal emulator. R STDOUT is parsed and numbers, negative numbers, dates in the standard format, strings, and R constants are identified…

r-colorramps 2.3

This package provides features to build gradient color maps. …

r-colorspace 1.4-1

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL…

r-colourpicker 1.0

This package provides a color picker that can be used as an input in Shiny apps or Rmarkdown documents. The color picker supports alpha opacity, custom color palettes, and many more…

r-combinat 0.0-8

This package provides assorted routines for combinatorics. …

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 2.4.3

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 2.0-0

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

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-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 1.52.0

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

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 1.28.0

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

r-copywriter 2.20.0

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 1.6.9

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 0.84

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 1.26.0

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 3.5.0

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 1.1.0

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 0.2.1

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 1.3.4

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-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 1.1.0.1

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-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 1.62.0

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

r-cubature 2.0.4.1

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 2.30.0

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

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-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 2.0.3

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

r-cytoml 2.0.5

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

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 0.9.0

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 3.1-27

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 2.0

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 1.13.0

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-dbi 1.1.0

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 1.4.4

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-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-delayedarray 0.14.1

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 1.10.1

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 0.1-29

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-dendextend 1.14.0

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-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 1.0-8

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 1.4.1

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-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 4.0.1

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 1.2.0

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 1.28.1

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 3.2.0

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

r-devtools 2.3.1

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

r-dexseq 1.34.1

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 1.6.4

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 0.0.8

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 2.16.0

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

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 0.6.25

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. …

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