Packages — R (Page 11 of 58)

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r-lattice 0.20-45

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also…

r-latticeextra 0.6-29

Building on the infrastructure provided by the lattice package, this package provides several new high-level graphics functions and methods, as well as additional utilities such as panel and axis annotation functions. …

r-lava 1.6.10

This package provides tools for the estimation and simulation of latent variable models. …

r-lavaan 0.6-11

This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models. …

r-lazyeval 0.2.2

This package provides the tools necessary to do non-standard evaluation (NSE) in R. …

r-lda 1.4.2

This package implements "latent Dirichlet allocation" (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is…

r-ldblock 1.24.0

This package defines data structures for "linkage disequilibrium" (LD) measures in populations. Its purpose is to simplify handling of existing population-level data for the purpose of flexibly defining LD blocks. …

r-ldheatmap 1.0-4

This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map…

r-leaflet 2.1.1

Create and customize interactive maps using the Leaflet JavaScript library and the `htmlwidgets' package. These maps can be used directly from the R console, from RStudio, in Shiny applications and R…

r-leaflet-providers 1.9.0

This package contains third-party map tile provider information from Leaflet.js, to be used with the `leaflet' R package. Additionally, `leaflet.providers' enables users to retrieve up-to-date provider information between package updates. …

r-leaps 3.1

This package provides tools for regression subset selection, including exhaustive search. …

r-learnbayes 2.15.1

This package provides a collection of functions helpful in learning the basic tenets of Bayesian statistical inference. It contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions.…

r-learnr 0.10.1

This package provides tools to create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages. …

r-leiden 0.3.9

This package implements the Python `leidenalg' module to be called in R. It enables clustering using the Leiden algorithm for partitioning a graph into communities. See also Traag et al…

r-leidenbase 0.1.3-1.430f22a

This package provides an R to C interface that runs the Leiden community detection algorithm to find a basic partition. It runs the equivalent of the `find_partition' function. This package…

r-lemon 0.4.5

This package provides functions for working with legends and axis lines of ggplot2, facets that repeat axis lines on all panels, and some knitr extensions. …

r-lexicon 1.2.1

This package provides a collection of lexical hash tables, dictionaries, and word lists. …

r-lfa 1.24.0

"Logistic Factor Analysis" (LFA) is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. …

r-lgr 0.4.3

This package offers a flexible, feature-rich yet light-weight logging framework based on `R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, JSON,…

r-lhs 1.1.5

This package provides a number of methods for creating and augmenting Latin Hypercube Samples. …

r-libcoin 1.0-9

This package provides basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999). …

r-lifecycle 1.0.1

Manage the life cycle of your exported functions with shared conventions, documentation badges, and non-invasive deprecation warnings. The lifecycle package defines four development stages (experimental, maturing, stable, and questioning) and three deprecation…

r-liger 0.4.2

LIGER is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors. …

r-lightgbm 3.3.2

Tree based algorithms can be improved by introducing boosting frameworks. LightGBM is one such framework, based on Ke, Guolin et al. (2017). This package offers an R interface to work…

r-lim 1.4.6

This package provides functions that read and solve linear inverse problems (food web problems, linear programming problems). …

r-limma 3.50.3

This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods…

r-limsolve 1.5.6

This package provides functions that: 1. find the minimum/maximum of a linear or quadratic function, 2. sample an underdetermined or overdetermined system, 3. solve a linear system…

r-linnorm 2.18.0

Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to…

r-linprog 0.9-4

This package can be used to solve Linear Programming / Linear Optimization problems by using the simplex algorithm. …

r-lintr 2.0.1

This package checks adherence to a given style, syntax errors and possible semantic issues. It supports on the fly checking of R code edited with `RStudio IDE', `Emacs' and `Vim'. …

r-lisreltor 0.1.4

This is an unofficial package aimed at automating the import of LISREL output in R. …

r-listenv 0.8.0

This package implements list environments. List environments are environments that have list-like properties. For instance, the elements of a list environment are ordered and can be accessed and iterated over…

r-lmds 0.1.0

This package provides a fast dimensionality reduction method scaleable to large numbers of samples. "Landmark Multi-Dimensional Scaling" (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete…

r-lme4 1.1-29

This package provides fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++…

r-lmertest 3.1-3

This package provides p-values in type I, II or III anova and summary tables for `lmer' model fits via Satterthwaite's degrees of freedom method. A Kenward-Roger method is also available via…

r-lmodel2 1.7-3

This package computes model II simple linear regression using "ordinary least squares" (OLS), "major axis" (MA), "standard major axis" (SMA), and "ranged major axis" (RMA). …

r-lmom 2.8

This package provides functions related to L-moments: computation of L-moments and trimmed L-moments of distributions and data samples; parameter estimation; L-moment ratio diagram; plot vs. quantiles of an extreme-value distribution. …

r-lmoments 1.3-1

This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial…

r-lmtest 0.9-40

This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided. …

r-lobstr 1.1.1

This package provides a set of tools for inspecting and understanding R data structures inspired by `str'. It includes `ast' for visualizing abstract syntax trees, `ref' for showing shared references, `cst'…

r-locfdr 1.1-8

This package can be used to compute local false discovery rates. …

r-locfit 1.5-9.5

This package provides functions used for local regression, likelihood and density estimation. …

r-locpol 0.7-0

Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators. …

r-logger 0.2.2

Inspired by the the `futile.logger' R package and `logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead. …

r-logspline 2.1.16

Contains routines for logspline density estimation. The function `oldlogspline()' uses the same algorithm as the logspline package version 1.0.x; i.e. the Kooperberg and Stone (1992) algorithm (with an improved interface). The…

r-longitudinal 1.1.13

This package contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical…

r-loo 2.5.1

This package provides an implementation of efficient approximate "leave-one-out" (LOO) cross-validation for Bayesian models fit using Markov chain Monte Carlo, as described in `doi:10.1007/s11222-016-9696-4'. The approximation uses "Pareto smoothed importance sampling" (PSIS),…

r-lpme 1.1.2

Provide nonparametric methods for mean regression model, modal regression and conditional density estimation in the presence/absence of measurement error. Bandwidth selection is also provided for each method. …

r-lpsolve 5.6.15

Lp_solve is software for solving linear, integer and mixed integer programs. This implementation supplies a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems. …

r-lpsymphony 1.22.0

This package was derived from Rsymphony. The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is…

r-lsa 0.73.2

The basic idea of latent semantic analysis (LSA) is, that text do have a higher order (=latent semantic) structure which, however, is obscured by word usage (e.g. through the use of…

r-lsd 4.1-0

This package creates lots of colorful plots in a multitude of variations. Try a demo of the LSD by running `demotour()'. …

r-lsei 1.3-0

It contains functions that solve least squares linear regression problems under linear equality/inequality constraints. Functions for solving quadratic programming problems are also available, which transform such problems into least squares ones first. …

r-ltm 1.2-0

This is a package supporting the analysis of multivariate dichotomous and polytomous data using latent trait models under the Item Response Theory approach. It includes the Rasch, the Two-Parameter Logistic, the…

r-lubridate 1.8.0

This package provides functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and…

r-lumi 2.46.0

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at…

r-lwgeom 0.2-8

Access to selected functions found in liblwgeom (https://github.com/postgis/postgis/tree/master/liblwgeom), the light-weight geometry library used by PostGIS (http://postgis.net/). …

r-m3c 1.16.0

M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of `K' and can reject the null hypothesis `K=1'. …

r-maftools 2.10.0

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature…

r-magic 1.6-0

This package provides a collection of efficient, vectorized algorithms for the creation and investigation of magic squares and hypercubes, including a variety of functions for the manipulation and analysis of arbitrarily dimensioned arrays. …

r-magick 2.7.3

This package provides bindings to ImageMagick, a comprehensive image processing library. It supports many common formats (PNG, JPEG, TIFF, PDF, etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). …

r-magrittr 2.0.3

Magrittr provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. …

r-maldiquant 1.21

This package provides a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely…

r-manipulatewidget 0.11.1

This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. …

r-mapplots 1.5.1

This package helps you create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying…

r-mapproj 1.2.8

This package converts latitude/longitude into projected coordinates. …

r-maps 3.4.0

This package provides an R module for display of maps. Projection code and larger maps are in separate packages (`mapproj' and `mapdata'). …

r-maptools 1.1-3

This package provides a set of tools for manipulating and reading geographic data, in particular ESRI Shapefiles. It includes binary access to GSHHG shoreline files. The package also provides interface…

r-markdown 1.1

This package provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. …

r-marray 1.72.0

This package contains class definitions for two-color spotted microarray data. It also includes functions for data input, diagnostic plots, normalization and quality checking. …

r-mass 7.3-56

This package provides functions and datasets for the book "Modern Applied Statistics with S" (4th edition, 2002) by Venables and Ripley. …

r-massspecwavelet 1.60.1

The MassSpecWavelet package aims to process "Mass Spectrometry" (MS) data mainly through the use of wavelet transforms. It supports peak detection based on "Continuous Wavelet Transform" (CWT). …

r-mast 1.20.0

This package provides methods and models for handling zero-inflated single cell assay data. …

r-matrix 1.4-1

This package provides classes and methods for dense and sparse matrices and operations on them using LAPACK and SuiteSparse. …

r-matrix-utils 0.9.8

This package implements data manipulation methods such as `cast', `aggregate', and `merge'/`join' for Matrix and Matrix-like objects. …

r-matrixcalc 1.0-5

This package provides a collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for…

r-matrixextra 0.1.9-1

This package extends sparse matrix and vector classes from the Matrix package by providing: 1. Methods and operators that work natively on CSR formats (compressed sparse …

r-matrixgenerics 1.6.0

This package provides S4 generic functions modeled after the `matrixStats' API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are…

r-matrixmodels 0.5-0

This package models with sparse and dense matrix matrices, using modular prediction and response module classes. …

r-matrixstats 0.61.0

This package provides methods operating on rows and columns of matrices, e.g. `rowMedians()', `rowRanks()', and `rowSds()'. There are also some vector-based methods, e.g. `binMeans()', `madDiff()' and `weightedMedians()'. All methods have…

r-maxlik 1.5-2

This package provides functions for "Maximum Likelihood" (ML) estimation, non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results…

r-maxstat 0.7-25

This package provides maximally selected rank statistics with several p-value approximations. …

r-mbess 4.9.0

This package implements methods that are useful in designing research studies and analyzing data, with particular emphasis on methods that are developed for or used within the behavioral, educational, and social sciences…

r-mbkmeans 1.10.0

This package implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation. …

r-mboost 2.9-6

This package provides a functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models…

r-mclust 5.4.9

This package provides Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference. …

r-mcmc 0.9-7

This package simulates continuous distributions of random vectors using "Markov chain Monte Carlo" (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are…

r-mcmcpack 1.6-2

This package contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library. …

r-mda 0.5-2

This is a package for mixture and flexible discriminant analysis, "multivariate adaptive regression splines" (MARS), BRUTO, and so on. …

r-megadepth 1.4.0

This package provides an R interface to Megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package,…

r-memoise 2.0.1

This R package caches the results of a function so that when you call it again with the same arguments it returns the pre-computed value. …

r-memuse 4.2-1

This package provides procedures to answer the following questions: How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is your current R session using? How…

r-metafor 2.4-0

This package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models…

r-metap 1.3

The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of…

r-metapod 1.2.0

This package implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in…

r-methylkit 1.20.0

MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from "Reduced representation bisulfite sequencing" (RRBS) and its…

r-methylumi 2.40.1

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent"…

r-metrics 0.1.4

This package provides an implementation of evaluation metrics in R that are commonly used in supervised machine learning. It implements metrics for regression, time series, binary classification, classification, and information retrieval problems.…

r-mgcv 1.8-40

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a `gam()' function, a wide variety of smoothers, JAGS support and…

r-mgsub 1.7.3

Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches). …

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