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

r-alakazam | public | Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>. | 2019-07-21 |

r-anomalydetection | public | Implements procedures developed by Gutierrez et al. (2017, <https://journal.r-project.org/archive/2017/RJ-2017-039/index.html>) to aid in detecting network log anomalies. By combining various multivariate analytic approaches relevant to network anomaly detection, it provides cyber analysts efficient means to detect suspected anomalies requiring further evaluation. | 2019-07-21 |

r-ahocorasicktrie | public | Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported. | 2019-07-21 |

r-arrow | public | R Integration to 'Apache' 'Arrow'. | 2019-07-21 |

r-arules | public | Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. | 2019-07-21 |

r-animation | public | Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily. SWF files generation not supported with this distribution | 2019-07-21 |

r-assotester | public | R package with statistical tests and methods for genetic association studies with emphasis on rare variants and binary (dichotomous) traits | 2019-07-21 |

r-apatables | public | A common task faced by researchers is the creation of APA style (i.e., American Psychological Association style) tables from statistical output. In R a large number of function calls are often needed to obtain all of the desired information for a single APA style table. As well, the process of manually creating APA style tables in a word processor is prone to transcription errors. This package creates Word files (.doc files) containing APA style tables for several types of analyses. Using this package minimizes transcription errors and reduces the number commands needed by the user. | 2019-07-21 |

r-ashr | public | The R package 'ashr' implements an Empirical Bayes approach for large-scale hypothesis testing and false discovery rate (FDR) estimation based on the methods proposed in M. Stephens, 2016, "False discovery rates: a new deal", <DOI:10.1093/biostatistics/kxw041>. These methods can be applied whenever two sets of summary statistics---estimated effects and standard errors---are available, just as 'qvalue' can be applied to previously computed p-values. Two main interfaces are provided: ash(), which is more user-friendly; and ash.workhorse(), which has more options and is geared toward advanced users. The ash() and ash.workhorse() also provides a flexible modeling interface that can accomodate a variety of likelihoods (e.g., normal, Poisson) and mixture priors (e.g., uniform, normal). | 2019-07-21 |

r-als | public | Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. Commonly applied constraints include unimodality, non-negativity, and normalization of components. Several data matrices may be decomposed simultaneously by assuming that one of the two matrices in the bilinear decomposition is shared between datasets. | 2019-07-21 |

r-anom | public | Analysis of means (ANOM) as used in technometrical computing. The package takes results from multiple comparisons with the grand mean (obtained with 'multcomp', 'SimComp', 'nparcomp', or 'MCPAN') or corresponding simultaneous confidence intervals as input and produces ANOM decision charts that illustrate which group means deviate significantly from the grand mean. | 2019-07-21 |

r-argonr | public | R wrapper around the argon HTML library. More at <https://demos.creative-tim.com/argon-design-system/>. | 2019-07-21 |

r-argparse | public | A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage. | 2019-07-21 |

r-aplpack | public | Some functions for drawing some special plots: The function 'bagplot' plots a bagplot, 'faces' plots chernoff faces, 'iconplot' plots a representation of a frequency table or a data matrix, 'plothulls' plots hulls of a bivariate data set, 'plotsummary' plots a graphical summary of a data set, 'puticon' adds icons to a plot, 'skyline.hist' combines several histograms of a one dimensional data set in one plot, 'slider' functions supports some interactive graphics, 'spin3R' helps an inspection of a 3-dim point cloud, 'stem.leaf' plots a stem and leaf plot, 'stem.leaf.backback' plots back-to-back versions of stem and leaf plot. | 2019-07-21 |

r-biganalytics | public | Extend the 'bigmemory' package with various analytics. Functions 'bigkmeans' and 'binit' may also be used with native R objects. For 'tapply'-like functions, the bigtabulate package may also be helpful. For linear algebra support, see 'bigalgebra'. For mutex (locking) support for advanced shared-memory usage, see 'synchronicity'. | 2019-07-21 |

r-argumentcheck | public | The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message. | 2019-07-21 |

r-asbio | public | Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0. | 2019-07-21 |

r-argparser | public | Cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script. | 2019-07-21 |

r-arsenal | public | An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document. | 2019-07-21 |

r-aroma.apd | public | DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.) | 2019-07-21 |

r-assertr | public | Provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. Similar to 'stopifnot()' but more powerful, friendly, and easier for use in pipelines. | 2019-07-21 |

r-ascii | public | Coerce R object to asciidoc, txt2tags, restructuredText, org, textile or pandoc syntax. Package comes with a set of drivers for Sweave. | 2019-07-21 |

r-attempt | public | Tools for defensive programming, inspired by 'purrr' mappers and based on 'rlang'.'attempt' extends and facilitates defensive programming by providing a consistent grammar, and provides a set of easy to use functions for common tests and conditions. 'attempt' only depends on 'rlang', and focuses on speed, so it can be easily integrated in other functions and used in data analysis. | 2019-07-21 |

pyfmmlib | public | Python wrappers for FMMLIB2D and FMMLIB3D | 2019-07-21 |

r-beanplot | public | Plots univariate comparison graphs, an alternative to boxplot/stripchart/violin plot. | 2019-07-21 |

r-base64 | public | Compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the 'openssl' or 'base64enc' package instead. | 2019-07-21 |

r-bcrocsurface | public | The bias-corrected estimation methods for the receiver operating characteristics ROC surface and the volume under ROC surfaces (VUS) under missing at random (MAR) assumption. | 2019-07-21 |

r-aws | public | We provide a collection of R-functions implementing adaptive smoothing procedures in 1D, 2D and 3D. This includes the Propagation-Separation Approach to adaptive smoothing as described in "J. Polzehl and V. Spokoiny (2006) <DOI:10.1007/s00440-005-0464-1>", "J. Polzehl and V. Spokoiny (2004) <DOI:10.20347/WIAS.PREPRINT.998>" and "J. Polzehl, K. Papafitsoros, K. Tabelow (2018) <DOI:10.20347/WIAS.PREPRINT.2520>", the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter. | 2019-07-21 |

r-basix | public | BASIX provides some efficient C/C++ implementations to speed up calculations in R. | 2019-07-21 |

r-bench | public | Tools to accurately benchmark and analyze execution times for R expressions. | 2019-07-21 |

r-bfa | public | Provides model fitting for several Bayesian factor models including Gaussian, ordinal probit, mixed and semiparametric Gaussian copula factor models under a range of priors. | 2019-07-21 |

r-bio3d | public | Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. | 2019-07-21 |

r-bigrquery | public | Easily talk to Google's 'BigQuery' database from R. | 2019-07-21 |

r-bestglm | public | Best subset glm using information criteria or cross-validation. Implements PCR and PLS using AIC/BIC. Implements one-standard deviation rule for use with the `caret` package. | 2019-07-21 |

r-bglr | public | Bayesian Generalized Linear Regression. | 2019-07-21 |

r-bezier | public | The bezier package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting. | 2019-07-21 |

r-autoplotly | public | Functionalities to automatically generate interactive visualizations for popular statistical results supported by 'ggfortify', such as time series, PCA, clustering and survival analysis, with 'plotly.js' <https://plot.ly/> and 'ggplot2' style. The generated visualizations can also be easily extended using 'ggplot2' and 'plotly' syntax while staying interactive. | 2019-07-21 |

r-autoshiny | public | Static code compilation of a 'shiny' app given an R function (into 'ui.R' and 'server.R' files or into a 'shiny' app object). See examples at <https://github.com/alekrutkowski/autoshiny>. | 2019-07-21 |

r-barcoder | public | Tools to generate unique identifiers and printable barcoded labels for sample management. The creation of unique ID codes and printable PDF files can be initiated by standard commands, user prompts, or through a GUI addin for R Studio. Both single-level and hierarchical labels can be created in the command line interactively or non-interactively. | 2019-07-21 |

r-aws.ec2metadata | public | Retrieve Amazon EC2 instance metadata from within the running instance. | 2019-07-21 |

r-batchjobs | public | Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page. | 2019-07-21 |

r-baseline | public | Collection of baseline correction algorithms, along with a framework and a GUI for optimising baseline algorithm parameters. Typical use of the package is for removing background effects from spectra originating from various types of spectroscopy and spectrometry, possibly optimizing this with regard to regression or classification results. Correction methods include polynomial fitting, weighted local smoothers and many more. | 2019-07-21 |

r-batch | public | Functions to allow you to easily pass command-line arguments into R, and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package. | 2019-07-21 |

r-bgmm | public | Two partially supervised mixture modeling methods: soft-label and belief-based modeling are implemented. For completeness, we equipped the package also with the functionality of unsupervised, semi- and fully supervised mixture modeling. The package can be applied also to selection of the best-fitting from a set of models with different component numbers or constraints on their structures. For detailed introduction see: Przemyslaw Biecek, Ewa Szczurek, Martin Vingron, Jerzy Tiuryn (2012), The R Package bgmm: Mixture Modeling with Uncertain Knowledge, Journal of Statistical Software <doi:10.18637/jss.v047.i03>. | 2019-07-21 |

r-betareg | public | Beta regression for modeling beta-distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of a beta-distributed response), bias-corrected and bias-reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided. | 2019-07-21 |

r-bigstep | public | Selecting linear and generalized linear models for large data sets using modified stepwise procedure and modern selection criteria (like modifications of Bayesian Information Criterion). Selection can be performed on data which exceed RAM capacity. | 2019-07-21 |

r-binhf | public | Binomial Haar-Fisz transforms for Gaussianization | 2019-07-21 |

r-biocmanager | public | A convenient tool to install and update Bioconductor packages. | 2019-07-21 |

r-biomark | public | Variable selection methods are provided for several classification methods | 2019-07-21 |

gdal | public | GDAL is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. | 2019-07-21 |

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