Packages — R (Page 8 of 25)

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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 1.16.0

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 0.99-7

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-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 0.3.3

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-lemon 0.4.3

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-lhs 1.0.1

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

r-libcoin 1.0-5

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

r-lifecycle 0.1.0

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-lim 1.4.6

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

r-limma 3.42.2

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 2.10.0

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 0.9-2

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-lme4 1.1-21

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 3.1-1

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-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 0.9-37

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-locfit 1.5-9.1

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

r-longitudinal 1.1.12

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-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 1.14.0

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-lsei 1.2-0

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 1.1-1

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 1.7.4

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 2.38.0

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-magic 1.5-9

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 2.3

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 1.5

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 1.19.3

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 0.10.0

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 1.2.7

This package converts latitude/longitude into projected coordinates. …

r-maps 3.3.0

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

r-maptools 0.9-9

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 1.64.0

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 7.3-51.5

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

r-massspecwavelet 1.52.0

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 1.12.0

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

r-matrix 1.2-18

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

r-matrix-utils 0.9.7

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

r-matrixcalc 1.0-3

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-matrixmodels 0.4-1

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

r-matrixstats 0.55.0

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-mclust 5.4.5

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 0.9-6.1

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-mda 0.4-10

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

r-memoise 1.1.0

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

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-methylkit 1.12.0

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 2.32.0

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-mgcv 1.8-31

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-mhsmm 0.4.16

The `r-mhsmm' package implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent…

r-mi 1.0

This package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of…

r-mice 3.8.0

Multiple imputation using "Fully Conditional Specification" (FCS) implemented by the MICE algorithm as described in http://doi.org/10.18637/jss.v045.i03 (Van Buuren and Groothuis-Oudshoorn (2011)). Each variable has its own imputation model. Built-in imputation models…

r-microbenchmark 1.4-7

This package provides infrastructure to accurately measure and compare the execution time of R expressions. …

r-mime 0.9

This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems. …

r-minfi 1.32.0

This package provides tools to analyze and visualize Illumina Infinium methylation arrays. …

r-minimal 3.6.2

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering.…

r-miniui 0.1.1.1

This package provides UI widget and layout functions for writing Shiny apps that work well on small screens. …

r-minpack-lm 1.2-1

The `nls.lm' function provides an R interface to `lmder' and `lmdif' from the MINPACK library, for solving nonlinear least-squares problems by a modification of the Levenberg-Marquardt algorithm, with support for lower and…

r-minqa 1.2.4

This package provides a derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell. …

r-misc3d 0.8-4

This package provides a collection of miscellaneous 3d plots, including isosurfaces. …

r-mitml 0.3-7

This package provides tools for multiple imputation of missing data in multilevel modeling. It includes a user-friendly interface to the packages pan and jomo, and several functions for visualization, data management…

r-mitools 2.4

This package provides tools to perform analyses and combine results from multiple-imputation datasets. …

r-mixomics 6.10.8

mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we…

r-mixtools 1.2.0

This package provides a collection of R functions for analyzing finite mixture models. …

r-mlbench 2.1-1

This package provides a collection of artificial and real-world machine learning benchmark problems, including, e.g., several data sets from the UCI repository. …

r-mlinterfaces 1.66.2

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers. …

r-mnormt 1.5-6

This package provides functions for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed…

r-modelmetrics 1.2.2.1

Written in C++ using `Rcpp', this package provides a collection of metrics for evaluating models. …

r-modelr 0.1.5

Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation. …

r-modeltools 0.2-22

This package provides a collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. …

r-moments 0.14

This package provides functions to calculate: moments, Pearson's kurtosis, Geary's kurtosis and skewness; it also includes tests related to them (Anscombe-Glynn, D'Agostino, Bonett-Seier). …

r-monocle 2.14.0

Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through…

r-monocle3 0.1.2

Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments. …

r-moonbook 0.2.3

This package provides several analysis-related functions for the book entitled "R statistics and graph for medical articles" (written in Korean), version 1, by Keon-Woong Moon with Korean demographic data with several plot…

r-mosaic 1.4.0

This package contain data sets and utilities from Project MOSAIC (http://mosaic-web.org) used to teach mathematics, statistics, computation and modeling. Project MOSAIC is a community of educators working to tie together aspects of…

r-mosaiccore 0.6.0

Common utilities used in other Mosaic family packages are collected here. …

r-mosaicdata 0.17.0

This package provides data sets from project Mosaic `http://mosaic-web.org' used to teach mathematics, statistics, computation and modeling. …

r-motifrg 1.30.0

This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods. …

r-motifstack 1.30.0

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it…

r-motiv 1.42.0

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can…

r-mpm 1.0-22

This is a package for exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis. …

r-msigdbr 7.0.1

This package provides the "Molecular Signatures Database" (MSigDB) gene sets typically used with the "Gene Set Enrichment Analysis" (GSEA) software in a standard R data frame with key-value pairs. Included are…

r-msir 1.3.2

This is an R package for dimension reduction based on finite Gaussian mixture modeling of inverse regression. …

r-msm 1.6.8

This package provides functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was designed for processes observed at arbitrary times in continuous time (panel data) but…

r-msnbase 2.12.0

This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data. …

r-msnid 1.20.0

This package extracts "tandem mass spectrometry" (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality…

r-multcomp 1.4-12

Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book…

r-multiassayexperiment 1.12.2

MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from `SummarizedExperiment', supporting an open-ended mix of standard…

r-multicool 0.1-11

This package provides a set of tools to permute multisets without loops or hash tables and to generate integer partitions. Cool-lex order is similar to colexicographical order. …

r-multidataset 1.14.0

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets…

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