Packages — R (Page 18 of 51)

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r-tm 0.7-8

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

r-tmaptools 3.1-1

Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates `tmap', the package for visualizing thematic…

r-tmb 1.7.21

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 2.44.0

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 0.2-12

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 3.3.3.1

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-tradeseq 1.6.0

This package provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on…

r-trajectoryutils 1.0.0

This package implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. It includes a function to create a cluster-level minimum spanning tree and data structures to hold…

r-transphylo 1.4.5

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-tree 1.0-41

This package provides procedures to work with classification and regression trees. …

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-treeio 1.16.2

This is an R package to make it easier to import and store phylogenetic trees with associated data; and to link external data from different sources to phylogeny. It also supports…

r-trend 1.1.4

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 0.10-48

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 0.1.6

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 1.3.3.1

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 2.3.3

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 1.0.2

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-dmelanogaster-ucsc-dm6-ensgene 3.12.0

This package exposes an annotation databases 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-tximeta 1.10.0

This package implements transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate…

r-tximport 1.20.0

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 1.0-4

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-tzdb 0.1.2

This package provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries,…

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-udunits2 0.13

This package provides simple bindings to Unidata's udunits library. …

r-umap 0.2.7.0

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 1.28.0

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 0.7-2

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-universalmotif 1.10.2

This package allows importing most common "specific structure" (motif) types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats…

r-univoutl 0.3

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-useful 1.2.6

This package provides a set of little functions that have been found useful to do little odds and ends such as plotting the results of K-means clustering, substituting special text characters, viewing…

r-usethis 2.0.1

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 1.2.2

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

r-uuid 0.1-4

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

r-uwot 0.1.10

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-v8 3.4.2

This package provides an R interface to V8: Google's JavaScript and WebAssembly engine. …

r-valr 0.6.3

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 1.22.0

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 1.38.0

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

r-variantfiltering 1.28.0

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 1.34.0

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 1.4-8

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-vcfr 1.12.0

This package facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R, a…

r-vctrs 0.3.8

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-vdiffr 1.0.2

This package is an extension to the testthat package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases. …

r-vegan 2.5-7

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 1.1-5

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 6.1.1

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 0.3.7

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 0.6.1

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 0.4.0

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-visdat 0.5.3

This package provides procedures to create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using `ggplot2'. …

r-vroom 1.5.5

This package reads and writes data files like CSV, TSV and FWF. When reading it uses a quick initial indexing step, then reads the values lazily, so only the data you…

r-vsn 3.60.0

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-waldo 0.3.1

Compare complex R objects and reveal the key differences. This package was designed particularly for use in testing packages where being able to quickly isolate key differences makes understanding test failures…

r-warp 0.2.0

This package provides tooling to group dates by a variety of periods including: yearly, monthly, by second, by week of the month, and more. The groups are defined in such a…

r-watermelon 1.36.0

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 2.26.0

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 1.8.2

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-wdman 0.2.5

There are a number of binary files associated with the Webdriver/Selenium project (see `http://www.seleniumhq.org/download/', `https://sites.google.com/a/chromium.org/chromedriver/', `https://github.com/mozilla/geckodriver', `http://phantomjs.org/download.html', and `https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver' for more information). This package provides functions to download these binaries and to manage processes involving…

r-webbioc 1.64.0

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…

r-webmockr 0.8.0

This is a package for stubbing and setting expectations on HTTP requests. It includes tools for stubbing HTTP requests, including expected request conditions and response conditions. You can match on…

r-webshot 0.5.2

Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and…

r-webutils 1.1

This package parses HTTP request data in `application/json', `multipart/form-data', or `application/x-www-form-urlencoded' format. It includes an example of hosting and parsing HTML form data in R using either `httpuv' or `Rhttpd'. …

r-weights 1.0.4

This package Provides a variety of functions for producing simple weighted statistics, such as weighted Pearson's correlations, partial correlations, Chi-Squared statistics, histograms, and t-tests. Also now includes some software for quickly recoding…

r-wesanderson 0.3.6

This package provides color palettes that have been generated mostly from Wes Anderson movies. …

r-wgaim 2.0-1

This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps. …

r-wgcna 1.70-3

This package provides functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. It includes functions for rudimentary data cleaning, construction and summarization of correlation networks, module identification and functions for…

r-whisker 0.4

This package provides logicless templating, with a syntax that is not limited to R. …

r-widgettools 1.70.0

This package contains tools to support the construction of tcltk widgets in R. …

r-wiggleplotr 1.16.0

This package provides tools to visualize read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of…

r-withr 2.4.2

This package provides a set of functions to run R code in an environment in which global state has been temporarily modified. Many of these functions were originally a part of…

r-wk 0.5.0

This package provides a minimal R and C++ API for parsing well-known binary and well-known text representation of geometries to and from R-native formats. Well-known binary is compact and fast to parse;…

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