## Packages — R (Page 1 of 16)

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### r 3.6.1

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-a3 1.0.0

This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward. …

### r-a4 1.32.0

This package provides a software suite for the automated analysis of Affymetrix arrays. …

### r-a4base 1.32.0

This package provides basic features for the automated analysis of Affymetrix arrays. …

### r-a4classif 1.32.0

This is the classification package for the automated analysis of Affymetrix arrays. …

### r-a4core 1.32.0

This is the core package for the automated analysis of Affymetrix arrays. …

### r-a4preproc 1.32.0

This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays. …

### r-a4reporting 1.32.0

This is a package for the automated analysis of Affymetrix arrays. It provides reporting features. …

### r-abadata 1.12.0

This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas: 1.…

### r-abaenrichment 1.14.1

The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function `aba_enrich' integrates the expression…

### r-abbyyr 0.5.5

This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine…

### r-abc 2.1

This package implements several "Approximate Bayesian Computation" (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate…

### r-abc-data 1.0

This package contains data which are used by functions of the abc package which implements several "Approximate Bayesian Computation" (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. …

### r-abcanalysis 1.2.1

Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to…

### r-abcoptim 0.15.0

Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle…

### r-abcp2 1.2

This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the…

### r-abcrf 1.8

This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models…

### r-abctools 1.1.3

This `r-abctools' package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods…

### r-abd 0.2-8

The `r-abd' package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter. …

### r-abe 3.0.1

This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select…

### r-abf2 0.7-1

This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported. …

### r-abhgenotyper 1.0.1

The `r-abhgenotyper' package provides simple imputation, error-correction and plotting capacities for genotype data. The package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline…

### r-abind 1.4-5

This package provides tools to combine multidimensional arrays into a single array. This is a generalization of `cbind' and `rbind'. It works with vectors, matrices, and higher-dimensional arrays. It…

### r-abjutils 0.2.3

This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal. …

### r-abn 2.1

Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model…

### r-abnormality 0.1.0

This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article "Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis". …

### r-abodoutlier 0.1

This package performs angle-based outlier detection on a given data frame. It offers three methods to process data: 1. full but slow implementation using all the data that has…

### r-abps 0.3

This package offers an implementation of the "Abnormal blood profile score" (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several…

### r-abseqr 1.2.0

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. AbseqR empowers the users of abseqPy with plotting and…

### r-absfiltergsea 1.5.1

This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA. …

### r-absim 0.2.6

This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion.…

### r-abundant 1.1

This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) `doi:10.1214/11-AOS962'. …

### r-ac3net 1.2.2

This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network. …

### r-aca 1.1

This package offers an interactive function for the detection of breakpoints in series. …

### r-acc 1.3.3

This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data. …

### r-accelerometry 3.1.2

This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the…

### r-accelmissing 1.4

This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also…

### r-acceptancesampling 1.0-6

This `r-acceptancesampling' provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans…

### r-acclma 1.0

This package contains a function that imports data from a file, or uses manually entered data from the format (x, y, weight) and plots the appropriate vs graph and graph. The…

### r-acd 1.5.3

This package provides tools for categorical data analysis with complete or missing responses. …

### r-acdm 1.0.4

ACDm is a package for Autoregressive Conditional Duration (ACD, Engle and Russell, 1998) models. It creates trade, price or volume durations from transactions (tic) data, performs diurnal adjustments, fits various ACD…

### r-acepack 1.4.1

This package provides ACE and AVAS methods for choosing regression transformations. …

### r-acsnminer 0.16.8.25

This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the "Atlas of Cancer Signalling Networks" (ACSN) or user imported maps.…

### r-activity 1.2

This package provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear…

### r-adaptivesparsity 1.6

This package implements the Figueiredo machine learning algorithm for adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models. …

### r-ade4 1.7-13

The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods. …

### r-adegenet 2.1.1

This package provides a toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and…

### r-adgoftest 0.3

This package provides an implementation of the Anderson-Darling GoF test with p-value calculation based on Marsaglia's 2004 paper "Evaluating the Anderson-Darling Distribution". …

### r-afex 0.24-1

This package provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. …

### r-affy 1.62.0

This package contains functions for exploratory oligonucleotide array analysis. …

### r-affyio 1.54.0

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats. …

### r-aggregation 1.0.1

This package contains functionality for performing the following methods of p-value aggregation: Fisher's method, the Lancaster method (weighted Fisher's method), and Sidak correction. …

### r-algdesign 1.1-7.3

This package provides tools to calculate exact and approximate theory experimental designs for D, A, and I criteria. Very large designs may be created. Experimental designs may be blocked or…

### r-all 1.26.0

The data consist of microarrays from 128 different individuals with "acute lymphoblastic leukemia" (ALL). A number of additional covariates are available. The data have been normalized (using rma) and it is…

### r-allelicimbalance 1.22.0

This package provides a framework for allele-specific expression investigation using RNA-seq data. …

### r-als 0.0.6

Alternating least squares is often used to resolve components contributing to data with a bilinear structure; the basic technique may be extended to alternating constrained least squares. This package provides an…

### r-amap 0.8-17

This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions). …

### r-analytics 3.0

This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test…

### r-annaffy 1.56.0

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. …

### r-annotate 1.62.0

This package provides R environments for the annotation of microarrays. …

### r-annotationdbi 1.46.0

This package provides user interface and database connection code for annotation data packages using SQLite data storage. …

### r-annotationfilter 1.8.0

This package provides classes and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters are used by `ensembldb', `Organism.dplyr', and other packages. …

### r-annotationforge 1.26.0

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi. …

### r-annotationfuncs 1.34.0

This package provides functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. `org.Bt.eg.db'). …

### r-annotationhub 2.16.0

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g. VCF, bed, wig) and other resources from standard…

### r-annotationtools 1.58.0

This package provides functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). …

### r-annotatr 1.10.0

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations…

### r-anota 1.32.0

Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level)…

### r-apcluster 1.4.7

This package implements affinity propagation clustering introduced by Frey and Dueck (2007). The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to…

### r-ape 5.3

This package provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences,…

### r-argparse 2.0.1

This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices. …

### r-argparser 0.4

This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an…

### r-arm 1.10-1

This package provides functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007. …

### r-aroma-light 3.14.0

This package provides methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or…

### r-arrmdata 1.18.0

This package provides raw beta values from 36 samples across 3 groups from Illumina 450k methylation arrays. …

### r-arrmnormalization 1.24.0

This is a package to perform the "Adaptive Robust Regression method" (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. …

### r-arules 1.6-3

This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat. …

### r-askpass 1.1

This package provides cross-platform utilities for prompting the user for credentials or a passphrase, for example to authenticate with a server or read a protected key. …

### r-aspi 0.2.0

This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections. …

### r-assertive 0.3-5

This package provides lots of predicates (`is_*' functions) to check the state of your variables, and assertions (`assert_*' functions) to throw errors if they aren't in the right form. …

### r-assertive-base 0.0-7

This package provides a minimal set of predicates and assertions used by the assertive package. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-code 0.0-3

This package provides a set of predicates and assertions for checking the properties of code. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-data 0.0-3

This package provides a set of predicates and assertions for checking the properties of (country independent) complex data types. This is mainly for use by other package developers who want to…

### r-assertive-data-uk 0.0-2

This package provides a set of predicates and assertions for checking the properties of UK-specific complex data types. This is mainly for use by other package developers who want to include…

### r-assertive-data-us 0.0-2

This package provides a set of predicates and assertions for checking the properties of US-specific complex data types. This is mainly for use by other package developers who want to include…

### r-assertive-datetimes 0.0-2

This package provides a set of predicates and assertions for checking the properties of dates and times. This is mainly for use by other package developers who want to include run-time…

### r-assertive-files 0.0-2

This package provides a set of predicates and assertions for checking the properties of files and connections. This is mainly for use by other package developers who want to include run-time…

### r-assertive-matrices 0.0-2

This package provides a set of predicates and assertions for checking the properties of matrices. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-models 0.0-2

This package provides a set of predicates and assertions for checking the properties of models. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-numbers 0.0-2

This package provides a set of predicates and assertions for checking the properties of numbers. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-properties 0.0-4

This package provides a set of predicates and assertions for checking the properties of variables, such as length, names and attributes. This is mainly for use by other package developers who…

### r-assertive-reflection 0.0-4

This package provides a set of predicates and assertions for checking the state and capabilities of R, the operating system it is running on, and the IDE being used. This is…

### r-assertive-sets 0.0-3

This package provides a set of predicates and assertions for checking the properties of sets. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-strings 0.0-3

This package provides a set of predicates and assertions for checking the properties of strings. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertive-types 0.0-3

This package provides a set of predicates and assertions for checking the types of variables. This is mainly for use by other package developers who want to include run-time testing features…

### r-assertthat 0.2.1

Assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that your code should satisfy, while also producing friendly error messages so that your users…

### r-atacseqqc 1.8.5

ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. …

### r-auc 0.3.0

This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the…

### r-aucell 1.6.1

AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a…

### r-backports 1.1.4

Provides implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with…