Packages — R (Page 12 of 58)

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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 3.14.0

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 4.1.3

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 0.9-1

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

r-misctools 0.6-26

This package provides miscellaneous small tools and utilities. Many of them facilitate the work with matrices, e.g. inserting rows or columns, creating symmetric matrices, or checking for semidefiniteness. Other…

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-mixedpower 2.0

Implementation of a simulation based aproach to power analysis. Mixedpower uses lotdata and a linear mixed model fitted with lme4 to simulate new data sets. wer is computed seperate for…

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 0.1-5

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 0.13.3

`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 0.5.2

`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 0.4.1

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 0.10.0

`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-mlr3ordinal 0.1.0-9000-0.9febac9

This package extends `mlr3' with support for performing ordinal regression. …

r-mlr3pipelines 0.4.0

`mlr3pipelines' enriches `mlr3' with a diverse set of pipelining operators (PipeOps) that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves…

r-mlr3tuning 0.13.0

`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 0.4.3

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 0.3.1

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 1.0-23

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 1.6.2

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 7.5.1

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 2.20.4

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 1.4-18

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-multcompview 0.1-8

Convert a logical vector or a vector of p-values or a correlation, difference, or distance matrix into a display identifying the pairs for which the differences were not significantly different. …

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 3.4.1

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 4.2.1

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. …

r-mvtnorm 1.1-3

This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities. …

r-mzid 1.32.0

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback…

r-mzr 2.28.0

The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for…

r-nabor 0.5.0

This package provides an R wrapper for libnabo, an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). `nabor' includes a `knn' function that…

r-naniar 0.6.1

Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. The package provides data structures and functions that facilitate the plotting of…

r-naturalsort 0.1.3

This package provides functions related to human natural ordering. It handles adjacent digits in a character sequence as a number so that natural sort function arranges a character vector by their…

r-nbclust 3.0

NbClust provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user. …

r-nbconvertr 1.3.2

This package calls the Jupyter script `nbconvert' to create vignettes from notebooks. Those notebooks (`.ipynb' files) are files containing rich text, code, and its output. Code cells can be edited…

r-nbpseq 0.3.0

This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data. …

r-ncdf4 1.19

This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata…

r-ncdfflow 2.40.0

This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data. …

r-ndjson 0.8.0

"Streaming JSON" (ndjson) has one JSON record per-line and many modern ndjson files contain large numbers of records. These constructs may not be columnar in nature, but it is often useful…

r-netrep 1.2.4

This package provides functions for assessing the replication/preservation of a network module's topology across datasets through permutation testing. …

r-network 1.17.1

This package provides tools to create and modify network objects. The `network' class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes. …

r-networkd3 0.4

This package creates D3 JavaScript network, tree, dendrogram, and Sankey graphs from R. …

r-nleqslv 3.3.2

The `r-nleqslv' package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are…

r-nlme 3.1-157

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models. …

r-nloptr 2.0.0

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available…

r-nlp 0.2-1

This package provides basic classes and methods for Natural Language Processing. …

r-nmf 0.24.0

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and…

r-nnet 7.3-17

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models. …

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