Packages — R (Page 2 of 52)

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r-adegenet 2.1.5

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 1.0-1

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

r-affxparser 1.66.0

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 1.72.0

This package contains functions for exploratory oligonucleotide array analysis. …

r-affycomp 1.70.0

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

r-affycompatible 1.54.0

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 1.52.0

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 1.66.0

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 1.64.0

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 1.32.0

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

r-alluvial 0.1-2

This package creates alluvial diagrams (also known as parallel sets plots) for multivariate and time series-like 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-altmeta 3.3

This package provides alternative statistical methods for meta-analysis, including: 1. bivariate generalized linear mixed models for synthesizing odds ratios, relative risks, and risk differences 2.…

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-aneufinder 1.22.0

This package implements functions for copy number variant calling, plotting, export and analysis from whole-genome single cell sequencing data. …

r-aneufinderdata 1.18.0

This package contains data used by `AneuFinder'. …

r-annaffy 1.66.0

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 1.72.0

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

r-annotationdbi 1.56.2

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

r-annotationfilter 1.18.0

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 1.36.0

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

r-annotationfuncs 1.40.0

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 3.2.0

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 1.68.0

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 1.20.0

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 1.42.0

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 1.16

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-antiword 1.3

Wraps the `AntiWord' utility to extract text from Microsoft Word documents. The utility only supports the old `doc' format, not the new xml based `docx' format. Use the `xml2' package to…

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 5.5

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-apeglm 1.16.0

This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients. …

r-aplot 0.1.1

Users may want to align plots with associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to align associated…

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 2.3.6

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-archr 1.0.0-1.46b519f

This package is designed to streamline scATAC analyses in R. …

r-argon2 0.4-0

This package provides utilities for secure password hashing via the argon2 algorithm. …

r-argparse 2.1.2

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 0.7.1

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 1.12-2

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 3.24.0

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 1.34.0

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-arrow 6.0.1

Apache Arrow is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. …

r-arsenal 3.6.3

This package provides an arsenal of R functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in R and RStudio and which use formulas and versatile…

r-arules 1.7-1

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-ascat 2.5.2

This package provides the ASCAT (Allele-Specific Copy Number Analysis of Tumors) R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles. …

r-asd 2.2

This package provdes means to run simulations for adaptive seamless designs with and without early outcomes for treatment selection and subpopulation type designs. …

r-ash 1.0-15

This package provides David Scott's ASH routines ported from S-PLUS to R. …

r-ashr 2.2-47

This package implements an empirical Bayes approach for large-scale hypothesis testing and false discovery rate estimation. …

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 0.2.8

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 0.3-6

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 0.0-9

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 0.0-3

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 0.0-5

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 2.8

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-astsa 1.14

This package provides data sets and scripts to accompany Time Series Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics,…

r-atacseqqc 1.18.0

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 1.16.0

AUCell identifies 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 critical subset…

r-aws 2.5-1

This package provides a collection of R-functions implementing adaptive smoothing procedures in 1D, 2D and 3D. This includes the Propagation-Separation approach to adaptive smoothing, the "Intersecting Confidence Intervals" (ICI), variational approaches, and…

r-aws-s3 0.3.21

This package provides a simple client package for the Amazon Web Services (AWS) Simple Storage Service (S3) REST API. …

r-aws-signature 0.6.0

This package generates version 2 and 4 request signatures for Amazon Web Services (AWS) and provides a mechanism for retrieving credentials from environment variables, AWS credentials files, and EC2 instance metadata. …

r-awsmethods 1.1-1

This package defines the generic method `extract' and provides `openMP' support as needed in several packages like `aws', `adimpro', `fmri', and `dwi'. …

r-babelgene 21.4

Genomic analysis of model organisms often requires the use of databases based on human data or making comparisons to patient-derived resources. This requires converting genes between human and non-human analogues. …

r-backports 1.3.0

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 1.22.0

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-ballgown 2.26.0

This package provides tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation. …

r-bamsignals 1.26.0

This package efficiently obtains 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-basilisk 1.6.0

This package installs a self-contained Conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages.…

r-basilisk-utils 1.6.0

This package implements utilities for installation of the basilisk package, primarily for creation of the underlying Conda instance. …

r-basix 1.1

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

r-batchelor 1.10.0

This package implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of…

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 0.9.15

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-battenberg 2.2.9

This package contains the Battenberg R package for subclonal copy number estimation, as described by Nik-Zainal et al. (doi:10.1016/j.cell.2012.04.023) …

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