Packages — R (Page 11 of 25)

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r-rgraphviz 2.30.0

This package interfaces R with the graphviz library for plotting R graph objects from the `graph' package. …

r-rhdf5 2.30.1

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata…

r-rhdf5lib 1.8.0

This package provides C and C++ HDF5 libraries for use in R packages. …

r-rhisat2 1.2.0

This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform…

r-rhpcblasctl 0.20-17

This package allows you to control the number of threads the BLAS library uses. It is also possible to control the number of threads in OpenMP. …

r-rhtslib 1.18.1

This package provides the HTSlib C library for high-throughput nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. …

r-riboprofiling 1.16.0

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of…

r-riboseqr 1.20.0

This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments. …

r-rintrojs 0.2.2

This package provides a wrapper for the Intro.js (http://www.introjs.com) library. This package makes it easy to include step-by-step introductions, and clickable hints in a Shiny application. It supports both static…

r-rio 0.5.16

This package provides streamlined data import and export infrastructure by making assumptions that the user is probably willing to make: `import' and `export' determine the data structure from the file extension, reasonable defaults…

r-ripseeker 1.26.0

This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a…

r-riverplot 0.6

Sankey plots are a type of diagram that is convenient to illustrate how flow of information, resources etc. separates and joins, much like observing how rivers split and merge. For…

r-rjags 4-10

This package provides an R interface to the JAGS MCMC library. JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain…

r-rjava 0.9-11

This package provides a low-level interface to the Java VM very much like .C/.Call and friends. It allows the creation of objects, calling methods and accessing fields. …

r-rjson 0.2.20

This package provides functions to convert R objects into JSON objects and vice-versa. …

r-rlang 0.4.4

This package provides a toolbox for working with base types, core R features like the condition system, and core `Tidyverse' features like tidy evaluation. …

r-rmarkdown 2.1

This package provides tools to convert R Markdown documents into a variety of formats. …

r-rmeta 3.0

This package provides functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. It draws standard summary plots, funnel plots, and computes summaries and tests for association and…

r-rmetasim 3.1.14

This package provides an interface between R and the metasim simulation engine. The simulation environment is documented in: Strand, A.(2002), Metasim 1.0: an individual-based environment for simulating population genetics of complex population dynamics. …

r-rmpfr 0.8-1

This package supports arithmetic (via S4 classes and methods) for arbitrary precision floating point numbers, including transcendental functions. To this end, the package interfaces with the "Multiple Precision Floating-Point Reliable" (MPFR) library. …

r-rmpi 0.6-9

This package provides an interface (wrapper) to MPI APIs. It also provides an interactive R manager and worker environment. …

r-rms 5.1-4

This is a package for regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. The rms package is a collection of functions…

r-rmtstat 0.3

This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices. …

r-rmysql 0.10.19

This package provides a DBI interface to MySQL / MariaDB. The RMySQL package contains an old implementation based on legacy code from S-PLUS which is being phased out. A modern…

r-rngtools 1.5

This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that…

r-rngwell 0.10-6

This is a dedicated package to WELL pseudo random generators, which were introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical…

r-rnifti 1.1.0

This package provides very fast read and write access to images stored in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between compiled C and interpreted R code. It also provides…

r-roar 1.22.0

This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments. …

r-robust 0.4-18.2

This package is a port of the S+ "Robust Library". It provides methods for robust statistics, notably for robust regression and robust multivariate analysis. …

r-robustbase 0.93-5

This package allows to analyze data with robust methods such as regression methodology including model selections and multivariate statistics. …

r-roc 1.62.0

This package provides utilities for "Receiver Operating Characteristic" (ROC) curves, with a focus on micro arrays. …

r-rocr 1.0-7

ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves…

r-rook 1.1-1

This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a `call' method or an…

r-rootsolve 1.8.2

This package provides routines to find the root of nonlinear functions, and to perform steady-state and equilibrium analysis of "ordinary differential equations" (ODE). It includes routines that: 1. generate gradient…

r-ropls 1.18.8

Latent variable modeling with "Principal Component Analysis" (PCA) and "Partial Least Squares" (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the…

r-rots 1.14.0

This package provides tools for calculating the "Reproducibility-Optimized Test Statistic" (ROTS) for differential testing in omics data. …

r-roxygen2 7.0.2

Roxygen2 is a Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE files. …

r-rpart 4.1-15

This package provides recursive partitioning functions for classification, regression and survival trees. …

r-rpostgresql 0.6-2

This package provides a Database Interface (DBI) compliant driver for R to access PostgreSQL database systems. …

r-rprojroot 1.3-2

This package helps accessing files relative to a project root. It provides helpers for robust, reliable and flexible paths to files below a project root. The root of a project is…

r-rprotobuflib 1.8.0

This package provides the headers and static library of Protocol buffers for other R packages to compile and link against. …

r-rqc 1.20.0

Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of…

r-rrcov 1.5-2

This package provides an implementation of robust location and scatter estimation and robust multivariate analysis with high breakdown point. …

r-rsamtools 2.2.2

This package provides an interface to the `samtools', `bcftools', and `tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files. …

r-rsbml 2.44.0

This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. …

r-rsofia 1.1

This package is a port of sofia-ml to R. Sofia-ml is a suite of fast incremental algorithms for machine learning that can be used for training models for classification or ranking. …

r-rsolnp 1.16

The Rsolnp package implements a general non-linear augmented Lagrange multiplier method solver, a "sequential quadratic programming" (SQP) based solver). …

r-rspectra 0.16-0

This package provides an R interface to the Spectra library for large-scale eigenvalue and SVD problems. It is typically used to compute a few eigenvalues/vectors of an n by n matrix,…

r-rsqlite 2.2.0

This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.8.2) is included. …

r-rstudioapi 0.11

This package provides functions to access the RStudio API and provide informative error messages when it's not available. …

r-rsubread 2.0.1

This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion…

r-rsvd 1.0.3

Low-rank matrix decompositions are fundamental tools and widely used for data analysis, dimension reduction, and data compression. Classically, highly accurate deterministic matrix algorithms are used for this task. However, the emergence…

r-rsvg 1.3

This package allows you to render vector-based SVG images into high-quality custom-size bitmap arrays using the librsvg2 library. The resulting bitmap can be written to e.g. PNG, JPEG or WEBP…

r-rtracklayer 1.46.0

rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user…

r-rtsne 0.15

This package provides an R wrapper around the fast T-distributed Stochastic Neighbor Embedding using a Barnes-Hut implementation. …

r-rttf2pt1 1.3.8

This package contains the program `ttf2pt1', for use with the `extrafont' package. …

r-runit 0.4.32

This package provides R functions implementing a standard unit testing framework, with additional code inspection and report generation tools. …

r-ruvseq 1.20.0

This package implements methods to "remove unwanted variation" (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples. …

r-rvcheck 0.1.7

This package provides tools to check the latest release version of R and R packages (on CRAN, Bioconductor or Github). …

r-rversions 2.0.1

This package provides functions to query the main R repository to find the versions that `r-release' and `r-oldrel' refer to, and also all previous R versions and their release dates. …

r-rvest 0.3.5

`r-rvest' helps you scrape information from web pages. It is designed to work with `magrittr' to make it easy to express common web scraping tasks, inspired by libraries like `BeautifulSoup'. …

r-s4vectors 0.24.3

The S4Vectors package defines the `Vector' and `List' virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily…

r-sampling 2.8

This package provides functions for drawing and calibrating samples. …

r-sandwich 2.5-1

This package provides model-robust standard error estimators for cross-sectional, time series, clustered, panel, and longitudinal data. …

r-sankeyd3 0.3.2-1.fd50a74

This package provides an R library to generate Sankey network graphs in R and Shiny via the D3 visualization library. …

r-sapa 2.0-2

This package provides software for the book Spectral Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden, Cambridge University Press, 1993. …

r-savr 1.24.0

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots. …

r-scales 1.1.0

This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends. …

r-scater 1.14.6

This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. …

r-scatterplot3d 0.3-41

This package provides an implementation of scatter plots for plotting. a three dimensional point cloud. …

r-scdd 1.10.0

This package implements a method to analyze single-cell RNA-seq data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two…

r-scde 1.99.2

The SCDE package implements a set of statistical methods for analyzing single-cell RNA-seq data. SCDE fits individual error models for single-cell RNA-seq measurements. These models can then be used for…

r-scone 1.10.0

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses. …

r-scran 1.14.6

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly…

r-scrime 1.3.5

This package provides tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). The main focus is on SNP data, but most of the…

r-sctransform 0.2.1

This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As…

r-sdmtools 1.1-221.2

This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time.…

r-seewave 2.1.5

This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and…

r-segmented 1.1-0

Given a regression model, segmented updates the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed. …

r-selectr 0.4-2

`r-selectr' translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. …

r-sendmailr 1.2-1

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R. …

r-seqbias 1.34.0

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads…

r-seqgl 1.1.4

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between…

r-seqinr 3.6-1

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system. …

r-seqlogo 1.52.0

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). …

r-seqminer 7.1

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R. …

r-seqpattern 1.18.0

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature. …

r-seriation 1.2-8

This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like…

r-servr 0.15

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory. …

r-sessioninfo 1.1.1

This package provides tools to query and print information about the current R session. It is similar to `utils::sessionInfo()', but includes more information about packages, and where they were installed from. …

r-sets 1.0-18

This package provides data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals. …

r-seurat 3.1.3

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality…

r-sf 0.8-1

This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to…

r-sfsmisc 1.1-5

This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics. …

r-sgseq 1.20.0

SGSeq is a package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice…

r-shades 1.4.0

This package provides functions for easily manipulating colors, creating color scales and calculating color distances. …

r-shape 1.4.4

This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ... …

r-shapes 1.2.5

This package provides routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See…

r-shiny 1.4.0

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful…

r-shinyace 0.4.1

This package provides Ace editor bindings to enable a rich text editing environment within Shiny. …

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