Packages — R (Page 11 of 52)

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### r-massspecwavelet 1.60.0

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 1.20.0

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

### r-matrix 1.3-4

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-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-maxstat 0.7-25

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

### 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 2.9-5

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 5.4.8

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 1.6-0

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 2.0.0

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-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 1.8-38

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). …

### r-mhg 1.1

This package runs a minimum-hypergeometric (mHG) test as described in "Discovering Motifs in Ranked Lists of DNA Sequences" by Eran Eden. …

### 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 3.13.0

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 1.4.9

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

### r-mime 0.12

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

### r-minet 3.52.0

This package implements various algorithms for inferring mutual information networks from data. …

### r-minfi 1.40.0

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

### r-minimal 4.1.2

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 0.9-1

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

### r-misha 4.1.0

This package is intended to help users to efficiently analyze genomic data resulting from various experiments. …

### r-mitml 0.4-3

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 6.18.1

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-mlapi 0.1.0

This package provides R6 abstract classes for building machine learning models with a scikit-learn like API. Scikit-learn is a popular module for the Python programming language whose design became a de…

### r-mlbench 2.1-3

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-mlearning 1.0-0

This package provides a unified interface to various machine learning algorithms. Confusion matrices are provided too. …

### 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 1.74.0

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

### r-mlr3 0.13.0

`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 0.5.1

`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 0.4.0

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 0.9.5

`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 0.9.0

`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-mmwrweek 0.1.3

The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. …

### 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-mockery 0.4.2

The two main functionalities of this package are creating mock objects (functions) and selectively intercepting calls to a given function that originate in some other function. It can be used with…

### r-model4you 0.9-7

This package provides procedures for model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects. Currently partitioning of linear models, `lm()', generalised…

### r-modeldata 0.1.1

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 2.22.0

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 1.0.0

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

### r-moonbook 0.2.4

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 1.8.3

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 0.9.0

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

### r-mosaicdata 0.20.2

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

### r-motifbreakr 2.8.0

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 1.36.0

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

### r-motifmatchr 1.16.0

Quickly find motif matches for many motifs and many sequences. This package wraps C++ code from the MOODS motif calling library. …

### 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 1.38.0

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…

### 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-mscoreutils 1.6.0

This package defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median…

### r-msfeatures 1.2.0

The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of…

### r-msigdbr 7.4.1

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 1.3.3

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

### r-msm 1.6.9

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-msmseda 1.32.0

Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors. …

### r-msmstests 1.32.0

This package provides statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and…

### r-msnbase 2.20.1

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

### r-msnid 1.28.0

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-mstate 0.3.2

Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models. …

### r-muhaz 1.2.6.4

This package produces a smooth estimate of the hazard function for censored data. …

### r-multcomp 1.4-17

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 1.20.0

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 0.1-12

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 1.22.0

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…

### r-multitaper 1.0-15

This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic…

### r-multtest 2.50.0

This package can do non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion…

### r-munsell 0.5.0

The Munsell package contains Functions for exploring and using the Munsell colour system. …

### r-mus-musculus 1.3.1

This package contains the `Mus.musculus' object to access data from several related annotation packages. …

### r-mutationalpatterns 3.4.0

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data. …

### r-mutoss 0.1-12

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package. …

### r-mvabund 4.1.12

This package provides a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. …

### r-mvcclass 1.68.0

This package contains classes used in model-view-controller (MVC) design. …