Packages — R (Page 14 of 33)

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r-squarem 2020.4

This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent…

r-stabledist 0.7-1

This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan. …

r-stabs 0.6-3

This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection…

r-stam 0.0-1

This package provides various methods to conduct Spatio-Temporal Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling. …

r-stanheaders 2.21.0-6

The C++ header files of the Stan project are provided by this package. There is a shared object containing part of the `CVODES' library, but it is not accessible from R.…

r-statcheck 1.3.0

This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies. …

r-statmod 1.4.34

This package provides a collection of algorithms and functions to aid statistical modeling. It includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss…

r-statnet-common 4.3.0

This package provides non-statistical utilities used by the software developed by the Statnet Project. …

r-stepwise 0.3

This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment. …

r-stm 1.3.5

The "Structural Topic Model" (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions. …

r-stopwords 2.0

This package provides multiple sources of stopwords, for use in text analysis and natural language processing. …

r-stringdist 0.9.6

This package implements an approximate string matching version of R's native `match' function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine,…

r-stringi 1.5.3

This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the…

r-stringr 1.4.0

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic `stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s…

r-strucchange 1.5-2

This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test…

r-styler 1.3.2

This is a package for pretty-printing R code without changing the user's formatting intent. …

r-subplex 1.6

This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy…

r-summarizedexperiment 1.18.2

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent…

r-summarytools 0.9.6

This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good…

r-suppdists 1.1-9.5

This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores…

r-survey 4.0

This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and…

r-survival 3.2-3

This package contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. …

r-survivalroc 1.0.3

Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344) …

r-survminer 0.4.8

This package contains the function `ggsurvplot()' for easily drawing beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot…

r-survmisc 0.5.5

This package provides a collection of functions to help in the analysis of right-censored survival data. These extend the methods available in the `survival' package. …

r-sushi 1.26.0

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures. …

r-sva 3.36.0

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are…

r-svdialogs 1.0.0

This package helps to construct standard dialog boxes for your GUI, including message boxes, input boxes, list, file or directory selection, and others. In case R cannot display GUI dialog boxes,…

r-svglite 1.2.3.2

`svglite' is a graphics device that produces clean "SVG" (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in `svg()', `svglite' is considerably faster,…

r-svgui 1.0.0

The SciViews `svGUI' package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets. It centralizes info about GUI elements currently used,…

r-svmisc 1.1.0

This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to `save()' or…

r-synchronicity 1.3.5

This package provides support for synchronization via mutexes and may eventually support interprocess communication and message passing. …

r-sys 3.4

This package provides drop-in replacements for the base `system2()' function with fine control and consistent behavior across platforms. It supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT /…

r-sysfonts 0.8.1

This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages. …

r-systemfonts 0.3.1

This package provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts'…

r-systempiper 1.22.0

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of "next generation sequence" (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features…

r-tab 4.1.1

This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional…

r-tam 3.5-19

This package includes tools for marginal maximum likelihood estimation and joint maximum likelihood estimation for unidimensional and multidimensional item response models. The package functionality covers the Rasch model, 2PL model, 3PL model,…

r-tcltk2 1.2-11

This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package …

r-tclust 1.4-1

This package implements different robust clustering algorithms (`tclust') based on trimming and including some graphical diagnostic tools (`ctlcurves' and `DiscrFact'). …

r-tdthap 1.1-11

Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". …

r-tea 1.1

This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the AMSE-criterion or at least by reducing the bias of the…

r-tensor 1.5

The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals. This package allows you to compute the…

r-tensora 0.36.1

This package provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate…

r-testthat 2.3.2

This package provides a unit testing system for R designed to be fun, flexible and easy to set up. …

r-tfisher 0.2.0

This package provides the "cumulative distribution function" (CDF), quantile, and statistical power calculator for a collection of thresholding Fisher's p-value combination methods, including Fisher's p-value combination method, truncated product method and, in particular,…

r-tfmpvalue 0.0.8

In putative "Transcription Factor Binding Sites" (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match scores. TFMPvalue provides the accurate calculation of a p-value with a score threshold…

r-tgconfig 0.0.0.9000-1.1e02c76

The goal of tgconfig is to provide infrastructure for managing package parameters. …

r-tgstat 1.0.2-1.4f8e60c

The goal of tgstat is to provide fast and efficient statistical tools. …

r-th-data 1.0-10

This package contains supporting data sets that are used in other packages maintained by Torsten Hothorn. …

r-threejs 0.3.3

Create interactive 3D scatter plots, network plots, and globes in R using the three.js visualization library. …

r-tibble 3.0.3

This package provides a `tbl_df' class that offers better checking and printing capabilities than traditional data frames. …

r-tidygraph 1.2.0

This package provides a graph implementation that can be thought of as two tidy data frames describing node and edge data respectively. It provides an approach to manipulate these two virtual…

r-tidymodels 0.1.1

The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. …

r-tidyposterior 0.0.3

This package can be used to conduct post hoc analyses of resampling results generated by models. For example, if two models are evaluated with the "root mean squared error" (RMSE) using…

r-tidypredict 0.4.6

This package parses a fitted R model object, and returns a formula in Tidy Eval code that calculates the predictions. It works with several database backends because it leverages `dplyr' and…

r-tidyr 1.1.2

tidyr is a reframing of the reshape2 package designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis. …

r-tidyselect 1.1.0

This package provides a backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with…

r-tidytext 0.2.5

This is a package for text mining for word processing and sentiment analysis using `dplyr', `ggplot2', and other Tidy tools. …

r-tidytree 0.3.3

Phylogenetic trees generally contain multiple components including nodes, edges, branches and associated data. This package provides an approach to convert tree objects to tidy data frames. It also provides tidy…

r-tidyverse 1.3.0

The `tidyverse' is a set of packages that work in harmony because they share common data representations and API design. This package is designed to make it easy to install and…

r-tiff 0.1-5

This package provides an easy and simple way to read, write and display bitmap images stored in the TIFF format. It can read and write both files and in-memory raw vectors. …

r-timedate 3043.102

This package provides an environment for teaching "Financial Engineering and Computational Finance" and for managing chronological and calendar objects. …

r-timeseriesexperiment 1.6.0

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for…

r-tinytex 0.25

This package provides helper functions to install and maintain the LaTeX distribution named TinyTeX, a lightweight, cross-platform, portable, and easy-to-maintain version of TeX Live. This package also contains helper functions to compile…

r-tm 0.7-7

This package provides a framework for text mining applications within R. …

r-tmb 1.7.18

With this tool, a user should be able to quickly implement complex random effect models through simple C++ templates. The package combines `CppAD' (C++ automatic differentiation), `Eigen' (templated matrix-vector library) and `CHOLMOD'…

r-tmvnsim 1.0-2

This package implements importance sampling from the truncated multivariate normal using the "Geweke-Hajivassiliou-Keane" (GHK) simulator. Unlike Gibbs sampling which can get stuck in one truncation sub-region depending on initial values, this package…

r-tokenizers 0.2.1

This is a package for converting natural language text into tokens. It includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, shingled characters, lines, tweets, Penn Treebank, regular…

r-tolerance 2.0.0

This package provides functions for estimating tolerance limits (intervals) for various univariate distributions (binomial, Cauchy, discrete Pareto, exponential, two-parameter exponential, extreme value, hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric, normal, Pareto, Poisson-Lindley, Poisson, uniform,…

r-topgo 2.40.0

The topGO package provides tools for testing "gene ontology" (GO) terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and…

r-topicmodels 0.2-11

This package provides an interface to the C code for "Latent Dirichlet Allocation" (LDA) models and "Correlated Topics Models" (CTM) by David M. Blei and co-authors and the C++ code for…

r-tractor-base 3.3.2

This package provides functions for working with magnetic resonance images. It supports reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualization; flexible image manipulation; metadata…

r-transphylo 1.4.4

This is a package to infer transmission trees from a dated phylogeny. It includes methods to simulate and analyze outbreaks. The methodology is described in Didelot et al. (2014)…

r-treeclust 1.1-7

This package provides tools to create a measure of inter-point dissimilarity useful for clustering mixed data, and, optionally, perform the clustering. …

r-trend 1.1.3

The analysis of environmental data often requires the detection of trends and change-points. This package includes tests for trend detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated) Hirsch-Slack Test, partial Mann-Kendall Trend…

r-triebeard 0.3.0

Radix trees, or tries, are key-value data structures optimized for efficient lookups, similar in purpose to hash tables. This package provides an implementation of radix trees for use in R programming…

r-triform 1.29.0

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics. …

r-trimcluster 0.1-5

The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points. …

r-truncnorm 1.0-8

This package provides functions for the truncated normal distribution with mean equal to `mean' and standard deviation equal to `sd'. It includes density, distribution, quantile, and expected value functions, as well…

r-tsa 1.3

This package contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan. …

r-tseries 0.10-47

This package provides functions relating to time series analysis and computational finance. …

r-tsne 0.1-3

This package provides a pure R implementation of the t-SNE algorithm. …

r-tsp 1.1-10

This package provides basic infrastructure and some algorithms for the "traveling salesperson problem"(TSP) (also known as the traveling salesman problem). …

r-ttr 0.24.2

This package provides functions and data to construct technical trading rules with R. …

r-tune 0.1.1

The ability to tune models is important. `tune' contains functions and classes to be used in conjunction with other `tidymodels' packages for finding reasonable values of hyper-parameters in models, pre-processing methods,…

r-tuner 1.3.3

This is a package for the analysis of music and speech. Analyze music and speech, extract features like MFCCs, handle wave files and their representation in various ways, read MP3, read…

r-tweedie 2.3.2

Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods. …

r-tweenr 1.0.1

In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for…

r-txdb-celegans-ucsc-ce6-ensgene 3.2.2

This package exposes a C elegans annotation database generated from UCSC by exposing these as TxDb objects. …

r-txdb-hsapiens-ucsc-hg19-knowngene 3.2.2

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as…

r-txdb-hsapiens-ucsc-hg38-knowngene 3.4.6

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg38 genome and based on the "knownGene" track. The database is exposed as…

r-txdb-mmusculus-ucsc-mm10-knowngene 3.10.0

This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC…

r-txdb-mmusculus-ucsc-mm9-knowngene 3.2.2

This package provides an annotation database of Mouse genome data. It is derived from the UCSC mm9 genome and based on the "knownGene" track. The database is exposed as a…

r-tximport 1.16.1

This package provides tools to import transcript-level abundance, estimated counts and transcript lengths, and to summarize them into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific…

r-txtplot 1.0-4

This package provides functions to produce rudimentary ASCII graphics directly in the terminal window. This package provides a basic plotting function (and equivalents of curve, density, acf and barplot) as well…

r-ucminf 1.1-4

This package provides an implementation of an algorithm for general-purpose unconstrained non-linear optimization. The algorithm is of quasi-Newton type with BFGS updating of the inverse Hessian and soft line search with…

r-umap 0.2.6.0

Uniform manifold approximation and projection is a technique for dimension reduction. This package provides an interface to the UMAP algorithm in R, including a translation of the original algorithm into R. …

r-unifiedwmwqpcr 1.24.0

This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. …

r-units 0.6-7

This package provides support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. It is compatible…

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