Packages — R (Page 5 of 58)

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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 0.4.14

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-circrnaprofiler 1.8.0

`r-circrnaprofiler' is a computational framework for a comprehensive in silico analysis of "circular RNA" (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection…

r-circular 0.4-94

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 2.1.0

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-cistopic-next 0.3.0-1.04cecbb

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 7.3-20

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 3.2.0

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 0.8.0

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-clubsandwich 0.5.5

Provides several cluster-robust variance estimators (i.e., sandwich estimators) for ordinary and weighted least squares linear regression models, including the bias-reduced linearization estimator introduced by Bell and McCaffrey (2002) `http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf' and developed further by Pustejovsky…

r-clue 0.3-60

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 2.1.3

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-clusterexperiment 2.14.0

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets. …

r-clusterprofiler 4.2.2

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

r-clusterr 1.2.6

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-clustree 0.4.4

Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number…

r-cmdfun 1.0.2

Writing interfaces to command line software is cumbersome. The cmdfun package provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line…

r-cmplot 4.0.0

Circle Manhattan Plot is an R package that can lay out genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's…

r-cmprsk 2.2-11

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-cner 1.30.0

This package provides tools for large-scale identification and advanced visualization of sets of conserved noncoding elements. …

r-cobs 1.3-4

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

r-coda 0.19-4

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 0.2-18

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

r-coin 1.4-2

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-collapsibletree 0.1.7

This is a package for interactive Reingold-Tilford tree diagrams created using D3.js, where every node can be expanded and collapsed by clicking on it. Tooltips and color gradients can be mapped to…

r-collections 0.3.5

This package provides high performance container data types such as queues, stacks, deques, dicts and ordered dicts. …

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 2.0-3

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 1.1.1

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 1.8.0

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 2.10.0

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 2.0-4

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 1.1.0

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 1.3.0

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 1.58.0

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-copykat 1.0.8-0.256de33

This package Copynumber KAryotyping of Tumors infers genomic copy number and subclonal structure of human tumors using integrative Bayesian approaches to identify genome-wide aneuploidy at 5MB resolution in single cells data. …

r-copynumber 1.34.0

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

r-copywriter 2.26.0

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-coro 1.0.2

This package provides coroutines for R, a family of functions that can be suspended and resumed later on. This includes async functions (which await) and generators (which yield). Async functions…

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 0.92

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 1.32.0

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 0.4.2

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 1.5.1

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 1.3.2

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 1.2.0

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 1.2.0

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 1.68.0

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

r-cubature 2.0.4.4

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 2.36.0

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 1.1.4

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 0.2-3

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-cycombine 0.2.6-1.f18504b

This package provides a method for combining single-cell cytometry datasets, which increases the analytical flexibility and the statistical power of the analyses while minimizing technical noise. …

r-cytobackbone 1.0.0-1.4c1a0a3

This package implements an algorithm which increases the number of simultaneously measurable markers and in this way helps with study of the immune responses. Thus, the present algorithm, named `CytoBackBone', allows…

r-cytolib 2.6.2

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

r-cytoml 2.6.0

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 3.2-13

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 2.4.0

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 1.14.2

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 0.1.4

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 0.4.0

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 1.1.2

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-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 1.6.0

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 2.22.0

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-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 1.40.0

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…

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