Packages — R (Page 6 of 11)

r-proc 1.13.0 — Display and analyze ROC curves

This package provides tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). The area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.

r-processx 3.2.0 — Execute and control system processes

This package provides portable tools to run system processes in the background. It can check if a background process is running; wait on a background process to finish; get the exit status of finished processes; kill background processes and their children; restart processes. It can read the standard output and error of the processes, using non-blocking connections. processx can poll a process for standard output or error, with a timeout. It can also poll several processes at once.

r-prodlim 2018.04.18 — Product-limit estimation for censored event history analysis

This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.

r-progress 1.2.0 — Terminal progress bars

This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS The package also provides a C++ API, that works with or without Rcpp.

r-promises 1.0.1 — Abstractions for promise-based asynchronous programming

This package provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to JavaScript promises, but with a syntax that is idiomatic R.

r-protgenerics 1.14.0 — S4 generic functions for proteomics infrastructure

This package provides S4 generic functions needed by Bioconductor proteomics packages.

r-proto 1.0.0 — Prototype object-based programming

Proto is an object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.

r-proxy 0.4-22 — Distance and similarity measures

This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

r-prroc 1.3.1 — Precision-Recall and ROC curves for weighted and unweighted data

This package computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method.

r-pryr 0.1.4 — Tools for computing on the R language

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

r-ps 1.2.1 — List, query, and manipulate system processes

The ps package implements an API to list, query, and manipulate system processes. Most of its code is based on the psutil Python package.

r-pscl 1.5.2 — Political science computational laboratory

The pscl is an R package providing classes and methods for:

  1. Bayesian analysis of roll call data (item-response models);

  2. elementary Bayesian statistics;

  3. maximum likelihood estimation of zero-inflated and hurdle models for count data;

  4. utility functions.

r-psych 1.8.10 — Procedures for psychological, psychometric, and personality research

This package provides a general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics.

r-purrr 0.2.5 — Functional programming tools

This package completes R's functional programming tools with missing features present in other programming languages.

r-pwr 1.2-2 — Basic functions for power analysis

This package provides power analysis functions along the lines of Cohen (1988).

r-qap 0.1-1 — Heuristics for the quadratic assignment problem (QAP)

This package implements heuristics for the quadratic assignment problem (QAP). Currently only a simulated annealing heuristic is available.

r-qdnaseq 1.18.0 — Quantitative DNA sequencing for chromosomal aberrations

The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

r-qtl 1.42-8 — R package for analyzing QTL experiments in genetics

R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl allows to estimate genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

r-quadprog 1.5-5 — Functions to solve quadratic programming problems

This package contains routines and documentation for solving quadratic programming problems.

r-quantmod 0.4-13 — Quantitative financial modelling framework

This package provides a quantitative financial modelling framework to allow users to specify, build, trade, and analyse quantitative financial trading strategies.

r-quantreg 5.36 — Quantile regression

This package provides an estimation and inference methods for models of conditional quantiles: linear and nonlinear parametric and non-parametric models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

r-quic 1.1 — Regularized sparse inverse covariance matrix estimation

This package implements the regularized Gaussian maximum likelihood estimation of the inverse of a covariance matrix. It uses Newton's method and coordinate descent to solve the regularized inverse covariance matrix estimation problem.

r-qvalue 2.14.0 — Q-value estimation for false discovery rate control

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local false discovery rate (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

r-r-cache 0.13.0 — Light-weight caching of objects and results

This package provides methods for caching or memoization of objects and results. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

r-r-methodss3 1.7.1 — S3 methods simplified

This package provides methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4.

r-r-oo 1.22.0 — R object-oriented programming with or without references

This package provides methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.

r-r-rsp 0.43.0 — Dynamic generation of scientific reports

The RSP markup language provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. Today's date is <%=Sys.Date()%>. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. RSP is ideal for self-contained scientific reports and R package vignettes.

r-r-utils 2.7.0 — Various programming utilities

This package provides utility functions useful when programming and developing R packages.

r-r2glmm 0.1.2 — Compute R squared for mixed (multilevel) models

This package computes model and semi partial R squared with confidence limits for the linear and generalized linear mixed model (LMM and GLMM). The R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM using penalized quasi-likelihood (PQL) estimation (see Jaeger et al. (2016)).

r-r4rna 0.1.4 — Analysis framework for RNA secondary structure

The R4RNA package aims to be a general framework for the analysis of RNA secondary structure and comparative analysis in R.

r-r6 2.3.0 — Classes with reference semantics in R

The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

r-radiant-data 0.9.7 — Data menu for Radiant: business analytics using R and Shiny

The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.

r-randomforest 4.6-14 — Breiman and Cutler's random forests for classification and regression

This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.

r-ranger 0.10.1 — Fast implementation of random forests

This package provides a fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently.

r-rann 2.6 — Fast nearest neighbour search

This package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. Provides approximate, exact searches, fixed radius searches, bd and kb trees.

r-rappdirs 0.3.1 — Determine where to save data, caches, and logs

This package provides an easy way to determine which directories on the user's computer should be used to save data, caches and logs. It is a port of Python's Appdirs to R.

r-rapportools 1.0 — Miscellaneous helper functions with sane defaults for reporting

This package provides helper functions that act as wrappers to more advanced statistical methods with the advantage of having sane defaults for quick reporting.

r-raremetals2 0.1 — Analyze gene-level association tests for binary trait

The R package rareMETALS2 is an extension of the R package rareMETALS. It was designed to meta-analyze gene-level association tests for binary trait. While rareMETALS offers a near-complete solution for meta-analysis of gene-level tests for quantitative trait, it does not offer the optimal solution for binary trait. The package rareMETALS2 offers improved features for analyzing gene-level association tests in meta-analyses for binary trait.

r-rbenchmark 1.0.0 — Benchmarking routine for R

This r-rbenchmark package is inspired by the Perl module Benchmark, and is intended to facilitate benchmarking of arbitrary R code. The library consists of just one function, benchmark, which is a simple wrapper around system.time. Given a specification of the benchmarking process (counts of replications, evaluation environment) and an arbitrary number of expressions, benchmark evaluates each of the expressions in the specified environment, replicating the evaluation as many times as specified, and returning the results conveniently wrapped into a data frame.

r-rbgl 1.58.0 — Interface to the Boost graph library

This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.

r-rbiofabric 0.3-1.666c2ae — BioFabric network visualization

This package provides an implementation of the function bioFabric for creating scalable network digrams where nodes are represented by horizontal lines, and edges are represented by vertical lines.

r-rcas 1.8.0 — RNA-centric annotation system

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

r-rcmdcheck 1.3.2 — Run R CMD check from R and capture results

Run R CMD check from R programmatically, and capture the results of the individual checks.

r-rcolorbrewer 1.1-2 — ColorBrewer palettes

This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at

r-rcpp 1.0.0 — Seamless R and C++ integration

The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.

r-rcppannoy 0.0.11 — Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors

Annoy is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from and save to disk. This package provides an R interface.

r-rcpparmadillo — Rcpp integration for the Armadillo linear algebra library

Armadillo is a templated C++ linear algebra library that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. This package includes the header files from the templated Armadillo library.

r-rcppeigen — Rcpp integration for the Eigen templated linear algebra library

This package provides an integration of Eigen in R using a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems.

r-rcppgsl 0.3.6 — Rcpp integration for GSL vectors and matrices

The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++.

r-rcppprogress 0.4.1 — Interruptible progress bar for C++ in R packages

This package allows to display a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

r-rcpproll 0.3.0 — Efficient rolling and windowed operations

This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.

r-rcurl 1.95-0.1.2 — General network client interface for R

The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, GET and POST forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

r-rdpack 0.10-1 — Update and manipulate Rd documentation objects

This package provides functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating Rd documentation for functions, methods and classes; it also includes Rd macros for citations and import of references from bibtex files for use in Rd files and roxygen2 comments, as well as many functions for manipulation of references and Rd files.

r-readr 1.1.1 — Read tabular data

This package provides functions to read flat or tabular text files from disk (or a connection).

r-readxl 1.1.0 — Read Excel files

This package lets you import Excel files into R. It supports .xls via the embedded libxls C library and .xlsx via the embedded RapidXML C++ library.

r-recipes 0.1.4 — Preprocessing tools to create design matrices

Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

r-refgenome 1.7.3 — Gene and splice site annotation using annotation data from Ensembl and UCSC

This package contains functionality for importing and managing of downloaded genome annotation data from the Ensembl genome browser (European Bioinformatics Institute) and from the UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.

r-regioner 1.14.0 — Association analysis of genomic regions

This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

r-registry 0.5 — Infrastructure for R package registries

This package provides a generic infrastructure for creating and using R package registries.

r-rematch 1.0.1 — Match regular expressions with a nicer API

This package provides a small wrapper on regexpr to extract the matches and captured groups from the match of a regular expression to a character vector.

r-remotes 2.0.2 — R package installation from remote repositories

Download and install R packages stored in GitHub, BitBucket, or plain subversion or git repositories. This package is a lightweight replacement of the install_* functions in the devtools package. Indeed most of the code was copied over from devtools.

r-reprex 0.2.1 — Prepare reproducible R code examples for sharing

This package provides a convenience wrapper that uses the rmarkdown package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites or email. reprex also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

r-reshape 0.8.8 — Flexibly reshape data

Flexibly restructure and aggregate data using just two functions: melt and cast. This package provides them.

r-reshape2 1.4.3 — Flexibly reshape data: a reboot of the "reshape" package

Reshape2 is an R library to flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

r-reticulate 1.10 — R interface to Python

This package provides an interface from R to Python modules, classes, and functions. When calling into Python, R data types are automatically converted to their equivalent Python types. When values are returned from Python to R they are converted back to R types.

r-rgl 0.99.16 — 3D visualization using OpenGL

This package provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

r-rgooglemaps 1.4.3 — Use Google Maps in R

This package serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R. This requires proper coordinate scaling.

r-rgraphviz 2.26.0 — Plotting capabilities for R graph objects

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

r-rhdf5 2.26.0 — HDF5 interface to R

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 on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

r-rhdf5lib 1.4.0 — HDF5 library as an R package

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

r-rhtslib 1.14.0 — High-throughput sequencing library as an R package

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 1.12.0 — Ribosome profiling data analysis

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 count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

r-riboseqr 1.16.0 — Analysis of sequencing data from ribosome profiling experiments

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

r-rio 0.5.10 — Swiss-army knife for data I/O

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 are used for data import and export (e.g., stringsAsFactors=FALSE), web-based import is natively supported (including from SSL/HTTPS), compressed files can be read directly without explicit decompression, and fast import packages are used where appropriate. An additional convenience function, convert, provides a simple method for converting between file types.

r-ripseeker 1.22.0 — Identifying protein-associated transcripts from RIP-seq experiments

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 suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

r-riverplot 0.6 — Sankey or ribbon plots

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 example, they can be used to compare different clusterings. This package provides an implementation of Sankey plots for R.

r-rjags 4-8 — Bayesian graphical models using MCMC

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 Monte Carlo (MCMC) simulation.

r-rjson 0.2.20 — JSON library for R

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

r-rlang — Functions for base types, core R and Tidyverse features

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 1.10 — Convert R Markdown documents into a variety of formats

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

r-rmpi 0.6-7 — R interface to message-passing interface (MPI)

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

r-rmtstat 0.3 — Distributions, statistics and tests derived from random matrix theory

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

r-rmysql 0.10.15 — Database interface and MySQL driver for R

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 MySQL client based on Rcpp is available from the RMariaDB package.

r-rngtools 1.3.1 — Utility functions for working with random number generators

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 are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

r-robust 0.4-18 — Port of the S+ "Robust Library"

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 0.93-3 — Basic robust statistics

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

r-rocr 1.0-7 — Visualizing the performance of scoring classifiers

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 from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism.

r-rook 1.1-1 — Web server interface for R

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 closure that takes exactly one argument, an environment, and returns a list with three named elements: the status, the headers, and the body.

r-rootsolve 1.7 — Tools for the analysis of ordinary differential equations

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 and jacobian matrices (full and banded),

  2. find roots of non-linear equations by the Newton-Raphson method,

  3. estimate steady-state conditions of a system of (differential) equations in full, banded or sparse form, using the Newton-Raphson method, or by dynamically running,

  4. solve the steady-state conditions for uni- and multicomponent 1-D, 2-D, and 3-D partial differential equations, that have been converted to ordinary differential equations by numerical differencing (using the method-of-lines approach).

r-rots 1.10.0 — Reproducibility-Optimized Test Statistic

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

r-roxygen2 6.1.1 — In-source documentation system for R

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

r-rpart 4.1-13 — Recursive partitioning and regression trees

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

r-rprojroot 1.3-2 — Finding files in project subdirectories

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 defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

r-rrcov 1.4-4 — Scalable robust estimators with high breakdown Point

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

r-rsamtools 1.34.0 — Interface to samtools, bcftools, and tabix

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-rsofia 1.1 — Port of sofia-ml to R

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 — General non-linear optimization

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

r-rsqlite 2.1.1 — SQLite interface for R

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 is included.

r-rstudioapi 0.8 — Safely access the RStudio API

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

r-rtracklayer 1.42.0 — R interface to genome browsers and their annotation tracks

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 may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.