Package Name | Access | Summary | Updated |
---|---|---|---|

r-mixomics | public | Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares. | 2019-07-20 |

r-precrec | public | Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves. | 2019-07-20 |

r-purrrlyr | public | Some functions at the intersection of 'dplyr' and 'purrr' that formerly lived in 'purrr'. | 2019-07-20 |

r-qtlrel | public | This software provides tools for quantitative trait mapping in populations such as advanced intercross lines where relatedness among individuals should not be ignored. It can estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for putative quantitative trait loci (QTL), and plot mapping results. It also has functions to calculate identity coefficients from pedigrees, especially suitable for pedigrees that consist of a large number of generations, or estimate identity coefficients from genotypic data in certain circumstances. | 2019-07-20 |

r-propr | public | An R package to calculate proportionality between vectors of compositional data | 2019-07-20 |

r-profvis | public | Interactive visualizations for profiling R code. | 2019-07-20 |

r-princurve | public | Fitting a principal curve to a data matrix in arbitrary dimensions. Hastie and Stuetzle (1989) <doi:10.2307/2289936>. | 2019-07-20 |

r-proxyc | public | Computes proximity between rows or columns of large matrices efficiently in C++. Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries. Among several built-in similarity/distance measures, computation of correlation, cosine similarity and Euclidean distance is particularly fast. | 2019-07-20 |

r-ptw | public | Parametric Time Warping aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation). Both warping of peak profiles and of peak lists are supported. | 2019-07-20 |

r-cyphr | public | Encryption wrappers, using low-level support from 'sodium' and 'openssl'. 'cyphr' tries to smooth over some pain points when using encryption within applications and data analysis by wrapping around differences in function names and arguments in different encryption providing packages. It also provides high-level wrappers for input/output functions for seamlessly adding encryption to existing analyses. | 2019-07-20 |

r-psychotools | public | Infrastructure for psychometric modeling such as data classes (for item response data and paired comparisons), basic model fitting functions (for Bradley-Terry, Rasch, parametric logistic IRT, generalized partial credit, rating scale, multinomial processing tree models), extractor functions for different types of parameters (item, person, threshold, discrimination, guessing, upper asymptotes), unified inference and visualizations, and various datasets for illustration. Intended as a common lightweight and efficient toolbox for psychometric modeling and a common building block for fitting psychometric mixture models in package "psychomix" and trees based on psychometric models in package "psychotree". | 2019-07-20 |

r-prettydoc | public | Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported. | 2019-07-20 |

r-prophet | public | Implements a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data. Prophet is robust to missing data and shifts in the trend, and typically handles outliers well. | 2019-07-20 |

r-prroc | public | 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. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>. | 2019-07-20 |

r-ppcor | public | Calculates partial and semi-partial (part) correlations along with p-value. | 2019-07-20 |

r-preseqr | public | Originally as an R version of Preseq <doi:10.1038/nmeth.2375>, the package has extended its functionality to predict the r-species accumulation curve (r-SAC), which is the number of species represented at least r times as a function of the sampling effort. When r = 1, the curve is known as the species accumulation curve, or the library complexity curve in high-throughput genomic sequencing. The package includes both parametric and nonparametric methods, as described by Deng C, et al. (2018) <arXiv:1607.02804v3>. | 2019-07-20 |

r-propcis | public | Computes two-sample confidence intervals for single, paired and independent proportions. | 2019-07-20 |

r-powerlaw | public | An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region. | 2019-07-20 |

r-probably | public | Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations. | 2019-07-20 |

r-qlcmatrix | public | Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC). | 2019-07-20 |

r-printr | public | Extends the S3 generic function knit_print() in 'knitr' to automatically print some objects using an appropriate format such as Markdown or LaTeX. For example, data frames are automatically printed as tables, and the help() pages can also be rendered in 'knitr' documents. | 2019-07-20 |

r-ptxqc | public | Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the MaxQuant software suite. Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format. Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) 'doi:10.1021/acs.jproteome.5b00780'. | 2019-07-20 |

r-qiimer | public | Open QIIME output files in R, compute statistics, and create plots from the data. | 2019-07-20 |

r-tsibbledata | public | Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted. | 2019-07-20 |

r-qtlcharts | public | Web-based interactive charts (using D3.js) for the analysis of experimental crosses to identify genetic loci (quantitative trait loci, QTL) contributing to variation in quantitative traits. | 2019-07-20 |

r-pvclust | public | An implementation of multiscale bootstrap resampling for assessing the uncertainty in hierarchical cluster analysis. It provides AU (approximately unbiased) p-value as well as BP (bootstrap probability) value for each cluster in a dendrogram. | 2019-07-20 |

harfbuzz | public | An OpenType text shaping engine. | 2019-07-20 |

r-rbamtools | public | Provides an R interface to functions of the 'SAMtools' C-Library by Heng Li <http://www.htslib.org/>. | 2019-07-20 |

r-ragg | public | Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG to use as alternative to the raster devices provided through the 'grDevices' package. | 2019-07-20 |

r-randomforestsrc | public | Fast OpenMP parallel computing of Breiman's random forests for survival, competing risks, regression and classification based on Ishwaran and Kogalur's popular random survival forests (RSF) package. Handles missing data and now includes multivariate, unsupervised forests, quantile regression and solutions for class imbalanced data. New fast interface using subsampling and confidence regions for variable importance. | 2019-07-20 |

r-rcppgsl | public | 'Rcpp' integration for 'GNU 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++. This package also serves as a prime example of how to build a package that uses 'Rcpp' to connect to another third-party library. The 'autoconf' script, 'inline' plugin and example package can all be used as a stanza to write a similar package against another library. | 2019-07-20 |

r-randomizr | public | Generates random assignments for common experimental designs and random samples for common sampling designs. | 2019-07-20 |

r-r.devices | public | Functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts. | 2019-07-20 |

r-radiant.data | public | 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. | 2019-07-20 |

r-quandl | public | Functions for interacting directly with the Quandl API to offer data in a number of formats usable in R, downloading a zip with all data from a Quandl database, and the ability to search. This R package uses the Quandl API. For more information go to <https://www.quandl.com/docs/api>. For more help on the package itself go to <https://www.quandl.com/help/r>. | 2019-07-20 |

r-r.filesets | public | A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first. | 2019-07-20 |

r-r.rsp | public | The RSP markup language makes any text-based document come alive. RSP 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. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes. | 2019-07-20 |

r-r.matlab | public | Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB. | 2019-07-20 |

pyjanitor | public | Python implementation of the R package janitor. | 2019-07-20 |

r-radix | public | Scientific and technical article format for the web. 'Radix' articles feature attractive, reader-friendly typography, flexible layout options for visualizations, and full support for footnotes and citations. | 2019-07-20 |

r-rcppcnpy | public | The 'cnpy' library written by Carl Rogers provides read and write facilities for files created with (or for) the 'NumPy' extension for 'Python'. Vectors and matrices of numeric types can be read or written to and from files as well as compressed files. Support for integer files is available if the package has been built with -std=c++11 which should be the default on all platforms since the release of R 3.3.0. | 2019-07-20 |

r-rainbow | public | Visualizing functional data and identifying functional outliers. | 2019-07-20 |

r-rcmdrmisc | public | Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R. | 2019-07-20 |

r-rcdk | public | Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D. | 2019-07-20 |

r-rafalib | public | A series of shortcuts for routine tasks originally developed by Rafael A. Irizarry to facilitate data exploration. | 2019-07-20 |

r-rchoicedialogs | public | Collection of portable choice dialog widgets | 2019-07-20 |

r-randtests | public | Several non parametric randomness tests for numeric sequences | 2019-07-20 |

r-rapport | public | Facilitating the creation of reproducible statistical report templates. Once created, rapport templates can be exported to various external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as the converter backend. | 2019-07-20 |

r-rationalexp | public | We implement a test of the rational expectations hypothesis based on the marginal distributions of realizations and subjective beliefs from D'Haultfoeuille, Gaillac, and Maurel (2018) <doi:10.3386/w25274>. This test can be used in cases where realizations and subjective beliefs are observed in two different datasets that cannot be matched, or when they are observed in the same dataset. The package also computes the estimator of the minimal deviations from rational expectations than can be rationalized by the data. | 2019-07-20 |

r-rclipboard | public | Leverages the functionality of 'clipboard.js', a JavaScript library for HMTL5-based copy to clipboard from web pages (see <https://clipboardjs.com> for more information), and provides a reactive copy-to-clipboard UI button component, called 'rclipButton', for 'shiny' R applications. | 2019-07-20 |

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