Packages — R (Page 9 of 39)

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r-lifecycle 0.2.0

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 3.46.0

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 2.14.0

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 1.1-26

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-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 0.9-38

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 1.5-9.4

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-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-loo 2.4.0

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 1.1.1

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 1.18.0

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-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 1.1-1

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 1.7.9.2

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 2.42.0

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-m3c 1.12.0

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-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 2.5.2

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 2.0.1

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 0.10.1

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 1.2.7

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 1.0-2

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 1.68.0

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 7.3-53

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

r-massspecwavelet 1.56.0

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 1.16.0

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 0.9.8

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-matrixgenerics 1.2.0

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 0.4-1

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

r-matrixstats 0.57.0

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-maxstat 0.7-25

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

r-mboost 2.9-3

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 5.4.7

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-mda 0.5-2

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

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-methylkit 1.16.0

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 2.36.0

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-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 1.8-33

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 3.12.0

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 1.36.0

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

r-minimal 4.0.3

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 0.9-0

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 6.14.0

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-mixsqp 0.3-43

This package provides an optimization method based on sequential quadratic programming for maximum likelihood estimation of the mixture proportions in a finite mixture model where the component densities are known. The…

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-mlecens 0.1-4

This package contains functions to compute the nonparametric "maximum likelihood estimator" (MLE) for the bivariate distribution of `(X,Y)', when realizations of `(X,Y)' cannot be observed directly. To be more precise, we…

r-mlinterfaces 1.70.0

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

r-mlr3 0.9.0

`mlr3' enables efficient, object-oriented programming on the building blocks of machine learning. It provides `R6' objects for tasks, learners, resamplings, and measures. The package is geared towards scalability and larger…

r-mlr3learners 0.4.3

`mlr3learners' extends `mlr3' and `mlr3proba' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest…

r-mlr3measures 0.3.0

This package implements multiple performance measures for supervised learning. It includes over 40 measures for regression and classification. Additionally, meta information about the performance measures can be queried, e.g. what…

r-mlr3misc 0.6.0

`mlr3misc' provides frequently used helper functions and assertions used in `mlr3' and its companion packages. It comes with helper functions for functional programming, for printing, to work with `data.table', as well…

r-mlr3tuning 0.5.0

`mlr3tuning' implements methods for hyperparameter tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various termination criteria can be set and combined. The class `AutoTuner' provides a convenient way…

r-mnormt 2.0.2

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-modeldata 0.1.0

This package provides data sets used for demonstrating or testing model-related packages. …

r-modelmetrics 1.2.2.2

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

r-modelr 0.1.8

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

r-modeltools 0.2-23

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 2.18.0

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 0.8.0

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

r-mosaicdata 0.20.1

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

r-motifbreakr 2.4.0

This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost…

r-motifdb 1.32.0

This package provides more than 2000 annotated position frequency matrices from nine public sources, for multiple organisms. …

r-motifrg 1.31.0

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

r-motifstack 1.34.0

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 1.43.0

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…

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