Packages — R (Page 9 of 32)
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r-mclust 5.4.6
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-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 1.14.2
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 2.34.0
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 1.8-31
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 3.11.0
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 1.34.0
This package provides tools to analyze and visualize Illumina Infinium methylation arrays. …
r-minimal 4.0.2
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 6.12.1
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-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 1.68.0
This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers. …
r-mnormt 2.0.1
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 1.2.2.2
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 2.16.0
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 0.18.0
This package provides data sets from project Mosaic `http://mosaic-web.org' used to teach mathematics, statistics, computation and modeling. …
r-motifbreakr 2.2.0
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 1.30.0
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 1.32.0
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-msigdbr 7.1.1
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 2.14.2
This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data. …
r-msnid 1.22.0
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 0.2.12
Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models. …
r-multcomp 1.4-13
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 1.14.0
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 0.1-11
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 1.16.0
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 1.0-14
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 2.44.0
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-mutationalpatterns 2.0.0
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 4.1.3
This package provides a set of tools for displaying, modeling and analysing multivariate abundance data in community ecology. …
r-mvtnorm 1.1-1
This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities. …
r-mzid 1.26.0
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 2.22.0
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-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 1.17
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 2.34.0
This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data. …
r-network 1.16.0
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 3.1-148
This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models. …
r-nloptr 1.2.2.2
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 0.2-0
This package provides basic classes and methods for Natural Language Processing. …
r-nmf 0.23.0
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 7.3-14
This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models. …
r-nnls 1.4
This package provides an R interface to the Lawson-Hanson implementation of an algorithm for "non-negative least squares" (NNLS). It also allows the combination of non-negative and non-positive constraints. …
r-noiseq 2.31.0
This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type…
r-nonnest2 0.5-5
This package allows for testing of non-nested models. It includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. The package…
r-nor1mix 1.3-0
This package provides S3 classes and methods for one-dimensional normal mixture models, for, e.g., density estimation or clustering algorithms research and teaching; it provides the widely used Marron-Wand densities. It also…
r-nortest 1.0-4
This package provides five omnibus tests for testing the composite hypothesis of normality. …
r-np 0.60-10
This package provides non-parametric (and semi-parametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. …
r-npsurv 0.4-0.1
This package contains functions for non-parametric survival analysis of exact and interval-censored observations. …
r-numderiv 2016.8-1.1
This package provides methods for calculating accurate numerical first and second order derivatives. …
r-oai 0.3.0
`oai' provides a general purpose client to work with any "Open Archives Initiative Protocol for 'Metadata' Harvesting" (OAI-PMH) service. Functions are provided to work with the OAI-PMH verbs: `GetRecord', `Identify', `ListIdentifiers', `ListMetadataFormats',…
r-oenb 0.0.1
Tools to access data from the data web service of the OeNB (Oesterreichische Nationalbank), `https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html'. …
r-officer 0.3.12
This package provides tools to access and manipulate Word and PowerPoint documents from R. The package focuses on tabular and graphical reporting from R; it also provides two functions that let…
r-oligo 1.52.0
This package provides a package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). …
r-oligoclasses 1.50.0
This package contains class definitions, validity checks, and initialization methods for classes used by the `oligo' and `crlmm' packages. …
r-ontologyindex 2.5
This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms. …
r-opencyto 2.0.0
This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy. …
r-openmx 2.17.4
This package allows for the estimation of a wide variety of advanced multivariate statistical models. It consists of a library of functions and optimizers that allow you to quickly and flexibly…
r-openssl 1.4.2
This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either…
r-openxlsx 4.1.5
This package simplifies the creation of Excel `.xlsx' files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to…
r-optparse 1.6.6
This package provides a command line parser inspired by Python's `optparse' library to be used with Rscript to write shebang scripts that accept short and long options. …
r-orddom 3.1
This package provides tools to compute ordinal, statistics and effect sizes as an alternative to mean comparison: Cliff's delta or success rate difference (SRD), Vargha and Delaney's A or the Area Under…
r-ordinal 2019.12-10
This package provides an implementation of cumulative link (mixed) models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered models. Estimation is…
r-ore 1.6.3
This package provides an alternative to R's built-in functionality for handling regular expressions, based on the Onigmo library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features. …
r-org-ce-eg-db 3.7.0
This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans. …
r-org-dm-eg-db 3.7.0
This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster. …
r-org-dr-eg-db 3.7.0
This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers. …