Packages — R (Page 13 of 25)

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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-sushi 1.24.0

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

r-sva 3.34.0

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

`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 3.3

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

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

r-systemfonts 0.1.1

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 1.20.0

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 3.3-10

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-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 2.3.1

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 2.1.3

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

r-tidygraph 1.1.2

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-tidyr 1.0.2

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 1.0.0

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-tidytree 0.3.1

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 1.4.0

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 0.19

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 1.7.16

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-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 2.38.1

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 0.2-9

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-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 1.1.2

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 1.28.0

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 1.2

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 1.1-9

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

r-ttr 0.23-6

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

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 3.4.7

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 1.14.0

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 1.0-3

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 0.2.4.1

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 1.22.0

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 0.6-5

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…

r-univoutl 0.1-5

This package provides well-known outlier detection techniques in the univariate case. Methods to deal with skewed distribution are included too. The Hidiroglou-Berthelot (1986) method to search for outliers in ratios…

r-untb 1.7-4

This package provides numerical simulations, and visualizations, of Hubbell's "Unified Neutral Theory of Biodiversity" (UNTB). …

r-upsetr 1.4.0

This package provides a more scalable alternative to Venn and Euler diagrams for visualizing intersecting sets. Create visualizations of intersecting sets using a novel matrix design, along with visualizations of several…

r-urca 1.3-0

This package provides unit root and cointegration tests encountered in applied econometric analysis. …

r-urltools 1.7.3

This package provides a toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorized. It…

r-usethis 1.5.1

This package helps you to automate R package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, GitHub integration, licenses,…

r-utf8 1.1.4

This package provides tools to process and print UTF-8 encoded international text (Unicode). Input, validate, normalize, encode, format, and display. …

r-uuid 0.1-2

This package provides tools for generating and handling of "Universally Unique Identifiers" (UUIDs). …

r-uwot 0.1.5

This package provides an implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018). It also provides means to transform new data and to carry…

r-valr 0.5.0

This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data. …

r-variancepartition 1.16.1

This is a package providing tools to quantify and interpret multiple sources of biological and technical variation in gene expression experiments. It uses a linear mixed model to quantify variation in…

r-variantannotation 1.32.0

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes. …

r-variantfiltering 1.22.0

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc. …

r-varianttools 1.28.0

Explore, diagnose, and compare variant calls using filters. The VariantTools package supports a workflow for loading data, calling single sample variants and tumor-specific somatic mutations or other sample-specific variant types (e.g., RNA…

r-varselrf 0.7-8

This package provides tools for the variable selection from random forests using both backwards variable elimination (for the selection of small sets of non-redundant variables) and selection based on the importance spectrum (somewhat…

r-vbsr 0.0.5

This package provides an efficient algorithm for solving ultra-sparse regularized regression models using a variational Bayes algorithm with a spike prior. The algorithm is solved on a path, with coordinate updates,…

r-vcd 1.4-5

This package provides visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was originally inspired…

r-vctrs 0.2.3

There are three main goals to the `vctrs' package: 1. To propose `vec_size()' and `vec_type()' as alternatives to `length()' and `class()'. These definitions are…

r-vegan 2.5-6

The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used…

r-velocyto 0.6-1.d779034

This package provides basic routines for estimation of gene-specific transcriptional derivatives and visualization of the resulting velocity patterns. …

r-venndiagram 1.6.20

This package provides a set of functions to generate high-resolution Venn and Euler plots. It includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and…

r-versions 0.3

This package allows you to install specified versions of R packages hosted on CRAN and provides functions to list available versions and the versions of currently installed packages. …

r-vgam 1.1-2

This package is an implementation of about 6 major classes of statistical regression models. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are…

r-vim 5.1.0

This package provides tools for the visualization of missing and/or imputed values are introduced, which can be used for exploring the data and the structure of the missing and/or imputed values. …

r-vioplot 0.3.4

This package provides a violin plot, which is a combination of a box plot and a kernel density plot. …

r-vipor 0.4.5

This package provides tools to generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom…

r-viridis 0.5.1

This package is a port of the new http://matplotlib.org/ (matplotlib) color maps (`viridis'--the default--, `magma', `plasma', and `inferno') to R. These color maps are designed in such a way that they…

r-viridislite 0.3.0

This package is a port of the new `matplotlib' color maps (`viridis', `magma', `plasma' and `inferno') to R. matplotlib is a popular plotting library for Python. These color maps are…

r-vsn 3.54.0

The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have…

r-watermelon 1.30.0

The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that…

r-wavcluster 2.20.0

This package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein…

r-waveslim 1.7.5.2

This package provides basic wavelet routines for time series (1D), image (2D) and array (3D) analysis. The code provided here is based on wavelet methodology developed in Percival and Walden (2000);…

r-wavetiling 1.28.0

This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models. …

r-webbioc 1.58.0

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by…

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