## Packages — R (Page 2 of 25)

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### r-adegenet 2.1.2

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 0.26-0

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

### r-affxparser 1.58.0

This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. …

### r-affy 1.64.0

This package contains functions for exploratory oligonucleotide array analysis. …

### r-affycomp 1.62.0

The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. …

### r-affycompatible 1.46.0

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx…

### r-affycontam 1.44.0

Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of…

### r-affycoretools 1.58.4

This package provides various wrapper functions that have been written to streamline the more common analyses that a Biostatistician might see. …

### r-affydata 1.32.0

This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package `affy'. …

### r-affyio 1.56.0

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-alabama 2015.3-1

Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization Algorithm; it is used for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed. …

### r-algdesign 1.2.0

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 1.24.0

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 0.8-18

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 1.58.0

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 1.64.0

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

### r-annotationdbi 1.48.0

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

### r-annotationfilter 1.10.0

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 1.28.0

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

### r-annotationfuncs 1.36.0

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 2.18.0

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 1.60.0

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 1.12.1

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 1.34.0

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-anthropometry 1.13

This package provides statistical methods especially developed to analyze anthropometric data. These methods are aimed at providing effective solutions to some commons problems related to Ergonomics and Anthropometry. They are based…

### r-apcluster 1.4.8

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-archetypes 2.2-0.1

The main function `archetypes' implements a framework for archetypal analysis supporting arbitrary problem solving mechanisms for the different conceptual parts of the algorithm. …

### r-archivist 2.3.4

Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different…

### 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 0.6

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 3.16.0

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 1.26.0

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 1.6-4

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-assertable 0.2.7

This package provides simple, flexible assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, `assertable' is tailored towards tabular data. It…

### 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-assertr 2.7

This package provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly. It is similar to `stopifnot()' but more…

### 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 1.10.2

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 1.8.0

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 1.1.5

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…

### r-bacon 1.14.0

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm…

### r-bamsignals 1.18.0

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of nucleotide sequence reads in given genomic ranges and it computes reads profiles and coverage profiles.…

### r-base64 2.0

This package is a compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the openssl or base64enc package instead. …

### r-base64enc 0.1-3

This package provides tools for handling Base64 encoding. It is more flexible than the orphaned "base64" package. …

### r-base64url 1.4

This package provides a URL-safe base64 encoder and decoder. In contrast to RFC3548, the 62nd character (`+') is replaced with `-', the 63rd character (`/') is replaced with `_'. Furthermore,…

### r-basix 1.1

BASIX provides some efficient C/C++ implementations of native R procedures to speed up calculations in R. …

### r-batchjobs 1.8

This package provides `Map', `Reduce' and `Filter' variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. …

### r-batchtools 0.9.12

As a successor of the packages BatchJobs and BatchExperiments, this package provides a parallel implementation of the Map function for high performance computing systems managed by various schedulers. A multicore and…

### r-bayesm 3.1-4

This package covers many important models used in marketing and micro-econometrics applications, including Bayes Regression (univariate or multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and Ordinal Probit, Multinomial Logit (MNL) and…

### r-bayesplot 1.7.1

This package provides plotting functions for posterior analysis, model checking, and MCMC diagnostics. The package is designed not only to provide convenient functionality for users, but also a common set of…

### r-bayestestr 0.5.2

This package provides utilities to understand and describe posterior distributions and Bayesian models. It includes point-estimates such as "Maximum A Posteriori" (MAP), measures of dispersion such as "Highest Density Interval" (HDI), and…

### r-bayseq 2.20.0

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods. …

### r-bbmisc 1.11

This package provides miscellaneous helper functions for the development of R packages. …

### r-bbmle 1.0.23.1

This package provides methods and functions for fitting maximum likelihood models in R. This package modifies and extends the `mle' classes in the `stats4' package. …

### r-bdgraph 2.62

This package provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. It uses a trans-dimensional "Markov Chain Monte Carlo" (MCMC) approach based on…

### r-bdsmatrix 1.3-4

This package provides procedures to work with block diagonal symmetric matrices, a special case of sparse matrices. …

### r-beachmat 2.2.1

This package provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices. …

### r-beanplot 1.2

This package provides beanplots, an alternative to boxplot/stripchart/violin plots. It can be used to plot univariate comparison graphs. …

### r-bedr 1.0.7

This package is for genomic regions processing using command line tools such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting…

### r-beeswarm 0.2.3

This package provides an implementation of bee swarm plots. The bee swarm plot is a one-dimensional scatter plot like stripchart, but with closely-packed, non-overlapping points. …

### r-bgmix 1.46.0

This package provides fully Bayesian mixture models for differential gene expression. …

### r-bgx 1.52.0

This package provides tools for Bayesian integrated analysis of Affymetrix GeneChips. …

### r-bh 1.72.0-3

This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages. …

### r-bhc 1.38.0

The method implemented in this package performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which…

### r-biased-urn 1.07

This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution). …

### r-biasedurn 1.07

This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution). …

### r-bibtex 0.4.2.2

This package provides a utility for R to parse a bibtex file. …

### r-bicare 1.44.0

This is a package for biclustering analysis and exploration of results. …

### r-biclust 2.0.2

The main function `biclust()' provides several algorithms to find biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax. In addition, the package provides methods for data preprocessing (normalization and discretization), visualization,…

### r-bifet 1.6.0

BiFET identifies "transcription factors" (TFs) whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the…

### r-biggr 1.22.0

This package provides an interface to simulate metabolic reconstruction from the BiGG database (http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates "flux balance analysis" (FBA) and the sampling of feasible flux…

### r-bigmelon 1.12.0

This package provides methods for working with Illumina arrays using the `gdsfmt' package. …

### r-bigmemory 4.5.36

This package provides methods to create, store, access, and manipulate large matrices. Matrices are allocated to shared memory and may use memory-mapped files. …

### r-bigmemory-sri 0.1.3

This package provides a shared resource interface for the bigmemory and synchronicity packages. …