Packages — R (Page 13 of 58)

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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 2.38.0

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 0.60-11

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 0.4.2

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 1.58.0

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 1.56.0

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

r-omnipathr 3.2.8

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 2.7

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

r-opencpu 2.2.7

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 2.6.0

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 2.0.0

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 2021-10.12

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 1.7.1

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-organismdbi 1.36.0

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-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…

r-ouch 2.17

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

r-outliers 0.15

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

r-overlap 0.3.4

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-packcircles 0.3.4

Algorithms to find arrangements of non-overlapping circles. …

r-packrat 0.7.0

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-pacman 0.5.1

This package provides tools to more conveniently perform tasks associated with add-on packages. `pacman' conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. …

r-palmerpenguins 0.1.0

This package includes size measurements, clutch observations, and blood isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins observed on islands in the Palmer Archipelago near Palmer Station, Antarctica. Data…

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 0.6.5

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 0.8.0

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-paralleldist 0.2.6

This package provides a fast parallelized alternative to R's native `dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of predefined distance functions from…

r-parallelly 1.31.0

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 0.17.0

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 1.3.0

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 0.2.1

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 1.2-15

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 1.1.1

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 1.34.0

`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-paws 0.1.12

This package provides an interface to Amazon Web Services, including storage, database, and compute services, such as Simple Storage Service (S3), DynamoDB NoSQL database, and Lambda functions-as-a-service. …

r-paws-analytics 0.1.12

This package provides an interface to Amazon Web Services analytics services, including Elastic MapReduce Hadoop and Spark big data service, Elasticsearch search engine, and more. …

r-paws-application-integration 0.1.12

This package provides an interface to Amazon Web Services application integration services, including Simple Queue Service (SQS) message queue, Simple Notification Service (SNS) publish/subscribe messaging, and more. …

r-paws-common 0.3.17

This package provides functions for making low-level API requests to Amazon Web Services. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build…

r-paws-compute 0.1.12

This package provides an interface to Amazon Web Services compute services, including Elastic Compute Cloud (EC2), Lambda functions-as-a-service, containers, batch processing, and more. …

r-paws-cost-management 0.1.12

This package provides an interface to Amazon Web Services cost management services, including cost and usage reports, budgets, pricing, and more. …

r-paws-customer-engagement 0.1.12

This package provides an interface to Amazon Web Services customer engagement services, including Simple Email Service, Connect contact center service, and more. …

r-paws-database 0.1.12

This package provides an interface to Amazon Web Services database services, including Relational Database Service (RDS), DynamoDB NoSQL database, and more. …

r-paws-developer-tools 0.1.12

This package provides an interface to Amazon Web Services developer tools services, including version control, continuous integration and deployment, and more. …

r-paws-end-user-computing 0.1.12

This package provides an interface to Amazon Web Services end user computing services, including collaborative document editing, mobile intranet, and more. …

r-paws-machine-learning 0.1.12

This package provides an interface to Amazon Web Services machine learning services, including SageMaker managed machine learning service, natural language processing, speech recognition, translation, and more. …

r-paws-management 0.1.12

This package provides an interface to Amazon Web Services management and governance services, including CloudWatch application and infrastructure monitoring, Auto Scaling for automatically scaling resources, and more. …

r-paws-networking 0.1.12

This package provides an interface to Amazon Web Services networking and content delivery services, including Route 53 Domain Name System service, CloudFront content delivery, load balancing, and more. …

r-paws-security-identity 0.1.12

This package provides an interface to Amazon Web Services security, identity, and compliance services, including the Identity and Access Management (IAM) service for managing access to services and resources, and more. …

r-paws-storage 0.1.12

This package provides an interface to Amazon Web Services storage services, including Simple Storage Service (S3). …

r-pbapply 1.5-0

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 0.3-7

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 0.5.1

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 1.86.0

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 1.9-74

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

r-pcatools 2.6.0

"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-pdftools 3.1.1

This package provides utilities based on `libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. It also supports high quality rendering of PDF documents into PNG, JPEG, TIFF…

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 1.1

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. …

r-performance 0.9.0

This package provides utilities for computing measures to assess model quality, which are not directly provided by R's `base' or `stats' packages. These include e.g. measures like r-squared, intraclass correlation…

r-performanceanalytics 2.0.4

This is a collection of econometric functions for performance and risk analysis. This package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. …

r-perm 1.0-0.2

This package provides several methods for performing permutation tests. It has three main functions, to perform linear permutation tests. These tests are tests where the test statistic is the sum…

r-permute 0.9-7

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). `permute' also allows split-plot designs,…

r-pfam-db 3.8.2

This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories. …

r-phangorn 2.8.1

Phangorn is a package for phylogenetic analysis in R. It supports estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. …

r-phantompeakqualtools 1.2.2-1.8d2b2d1

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these…

r-phastcons100way-ucsc-hg19 3.7.2

This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species. …

r-pheatmap 1.0.12

This package provides an implementation of heatmaps that offers more control over dimensions and appearance. …

r-phontools 0.2-2.1

This package contains tools for the organization, display, and analysis of the sorts of data frequently encountered in phonetics research and experimentation, including the easy creation of IPA vowel plots, and the…

r-phylobase 0.8.10

This package provides a base `S4' class for comparative methods, incorporating one or more trees and trait data. …

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