Packages — R (Page 10 of 39)

### Packages menu:

#### Browse alphabetically

### 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 1.2.0

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-msigdbr 7.2.1

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-msmseda 1.28.0

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 1.28.0

This packages 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 2.16.0

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

### r-msnid 1.24.0

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-muhaz 1.2.6.1

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

### r-multcomp 1.4-15

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 1.16.0

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 1.18.0

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 2.46.0

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 3.0.1

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 4.1.3

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 1.28.0

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 2.24.1

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-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 2.36.0

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

### r-network 1.16.1

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 3.1-150

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 0.2-1

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 2.34.0

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 0.5-0

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 0.3.15

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 1.54.1

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 1.52.0

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 2.2.0

This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy. …

### r-openmx 2.18.1

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 1.4.3

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 4.2.3

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-optimx 2020-4.2

This package provides a replacement and extension of the `optim' function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained…

### 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. …

### r-org-eck12-eg-db 3.12.0

This package provides genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers. Entrez Gene is National Center for Biotechnology Information (NCBI)’s database for gene-specific…

### r-org-hs-eg-db 3.7.0

This package contains genome-wide annotations for Human, primarily based on mapping using Entrez Gene identifiers. …

### r-org-mm-eg-db 3.7.0

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus. …

### r-organismdbi 1.32.0

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select…

### r-ouch 2.14-1

This package provides tools to fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree. …

### r-outliers 0.14

This package provides a collection of some tests commonly used for identifying outliers. …

### r-overlap 0.3.3

This package provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals. …

### r-packrat 0.5.0

This package provides a dependency manager for R projects that allows you to manage the R packages your project depends on in an isolated, portable, and reproducible way. …

### r-pamr 1.56.1

This package provides some functions for sample classification in microarrays. …

### r-pan 1.6

This package implements multiple imputation for multivariate panel or clustered data. …

### r-pander 0.6.3

The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex…

### r-paradox 0.6.0

With this package it is possible to define parameter spaces, constraints and dependencies for arbitrary algorithms, and to program on such spaces. It also includes statistical designs and random samplers. …

### r-parallelly 1.21.0

This package provides utility functions that enhance the `parallel' package and support the built-in parallel backends of the `future' package. For example, `availableCores' gives the number of CPU cores available to…

### r-parameters 0.10.1

This package provides utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models, this package implements features like…

### r-parcor 0.2-6

This package estimates the matrix of partial correlations based on different regularized regression methods: lasso, adaptive lasso, PLS, and Ridge Regression. In addition, the package provides model selection for lasso, adaptive lasso…

### r-parmigene 1.1.0

This package provides a parallel estimation of the mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for the reconstruction of gene regulatory networks. …

### r-parsedate 1.2.0

This package provides three functions for dealing with dates: `parse_iso_8601' recognizes and parses all valid ISO 8601 date and time formats, `parse_date' parses dates in unspecified formats, and `format_iso_8601' formats a date…

### r-parsnip 0.1.4

This package provides a common interface to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. R, Spark, Stan,…

### r-partitions 1.9-22

This package provides tools to enumerates the partitions, unequal partitions, and restricted partitions of an integer; the three corresponding partition functions are also given. …

### r-partykit 1.2-10

This package provides a toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. …

### r-pasilla 1.14.0

This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article 'Conservation of an RNA regulatory map between Drosophila and mammals' by…

### r-pastecs 1.3.21

This package provides functions for regulation, decomposition and analysis of space-time series. The `pastecs' library is a PNEC-Art4 and IFREMER initiative to bring PASSTEC 2000 functionalities to R. …

### r-patchwork 1.1.0

The `ggplot2' package provides a strong API for sequentially building up a plot, but does not concern itself with composition of multiple plots. Patchwork is a package that expands the API…

### r-pathview 1.30.1

`r-pathview' is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to…

### r-pbapply 1.4-3

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap. …

### r-pbdzmq 0.3-3.1

ZeroMQ is a well-known library for high-performance asynchronous messaging in scalable, distributed applications. This package provides high level R wrapper functions to easily utilize ZeroMQ. The main focus is on…

### r-pbivnorm 0.6.0

This package provides a vectorized R function for calculating probabilities from a standard bivariate normal CDF. …

### r-pbkrtest 0.4-8.6

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models. …

### r-pbmcapply 1.5.0

This light-weight package helps you track and visualize the progress of parallel versions of vectorized R functions of the `mc*apply' family. …

### r-pcamethods 1.82.0

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA,…

### r-pcapp 1.9-73

This package provides functions for robust "principal component analysis" (PCA) by projection pursuit. …

### r-pcatools 2.2.0

"Principal Component Analysis" (PCA) extracts the fundamental structure of the data without the need to build any model to represent it. This "summary" of the data is arrived at through a…

### r-pdist 1.2

Pdist computes the euclidean distance between rows of a matrix X and rows of another matrix Y. Previously, this could be done by binding the two matrices together and calling `dist',…

### r-pegas 0.14

This package provides functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage…

### r-penalized 0.9-51

This package provides tools for fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge)…

### r-perfmeas 1.2.1

This package implements different performance measures for classification and ranking tasks. "Area under curve" (AUC), precision at a given recall, F-score for single and multiple classes are available. …