Packages — R (Page 13 of 61)

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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 1.8.4

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 0.9.2

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

r-mosaicdata 0.20.3

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

r-motifbreakr 2.10.0

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 1.38.0

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

r-motifmatchr 1.18.0

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 1.40.0

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-mritc 0.5-2

This package provides various methods for MRI tissue classification. …

r-mscoreutils 1.8.0

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-msdata 0.36.0

This package provides Ion Trap positive ionization mode data in mzML file format. It includes a subset from 500-850 m/z and 1190-1310 seconds, including MS2 and MS3, intensity threshold 100.000; extracts…

r-msfeatures 1.4.0

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 1.34.0

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 1.34.0

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 2.22.0

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

r-msnid 1.30.0

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 1.4-20

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 1.22.0

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 1.24.0

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 2.52.0

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-mumin 1.47.1

Tools for performing model selection and model averaging. Automated model selection through subsetting the maximum model, with optional constraints for model inclusion. Model parameter and prediction averaging based on model weights…

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-muscat 1.10.1

This package `muscat' provides various methods and visualization tools for "DS"(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated "pseudobulk" data, as well as…

r-mutationalpatterns 3.6.0

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 4.2.1

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

r-mvcclass 1.70.0

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 1.34.0

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 2.30.0

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 3.0.1

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 0.3.1

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 2.42.1

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 1.17.2

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 3.3.3

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 3.1-159

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

r-nloptr 2.0.3

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. …

r-nnlm 0.4.4-1.4574bca

This is a package for "Non-Negative Linear Models" (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and "non-negative matrix factorization" (NMF). It supports mean square error…

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 2.40.0

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-norm 1.0-10.0

Multiple imputation of multivariate continuous data under a normal model. …

r-nortest 1.0-4

This package provides five omnibus tests for testing the composite hypothesis of normality. …

r-np 0.60-14

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-nsprcomp 0.5.1-2

This package implements two methods for performing a constrained principal component analysis (PCA), where non-negativity and/or sparsity constraints are enforced on the principal axes (PAs). The function `nsprcomp' computes one principal component…

r-numderiv 2016.8-1.1

This package provides methods for calculating accurate numerical first and second order derivatives. …

r-oai 0.3.2

`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 0.0.2

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 0.4.4

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 1.60.0

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 1.58.0

This package contains class definitions, validity checks, and initialization methods for classes used by the `oligo' and `crlmm' packages. …

r-omicade4 1.36.0

This package performes multiple co-inertia analysis of omics datasets. …

r-omnipathr 3.5.5-1.679bb79

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access…

r-omnipathr 3.4.0

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access…

r-ontologyindex 2.10

This package provides functions for reading ontologies into R as lists and manipulating sets of ontological terms. …

r-opencpu 2.2.8

This package provides a system for embedded scientific computing and reproducible research with R. The OpenCPU server exposes a simple but powerful HTTP API for RPC and data interchange with R.…

r-opencyto 2.8.4

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

r-openmx 2.20.6

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 2.0.3

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 4.2.5

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-optimx 2022-4.30

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 1.7.3

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 1.7.1.1

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-bt-eg-db 3.13.0

This package provides genome wide annotations for Bovine, primarily based on mapping using Entrez Gene identifiers. …

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 3.14.0

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-organism-dplyr 1.24.0

This package provides an alternative interface to Bioconductor `annotation' resources, in particular the gene identifier mapping functionality of the `org' packages (e.g., `org.Hs.eg.db') and the genome coordinate functionality of the `TxDb' packages (e.g.,…

r-organismdbi 1.38.1

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-orgmassspecr 0.5-3

This package `OrgMassSpecR' is an extension of the `R' statistical computing language. It contains functions to assist with organic or biological mass spectrometry data analysis. Mass spectral libraries are available…

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