Packages — R (Page 3 of 58)

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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 1.18.1

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 0.3.2

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 22.3

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-babelwhale 1.0.3

This package provides a unified interface to interact with Docker and Singularity containers. You can execute a command inside a container, mount a volume or copy a file. …

r-backports 1.4.1

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 1.9

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) …

r-bayesfactor 0.9.12-4.3

This package provides a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression. …

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 1.9.0

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 0.11.5

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 2.28.0

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 1.12

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

r-bbmle 1.0.24

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-bbotk 0.5.2

This package provides a common framework for optimization of black-box functions for other packages, e.g. `mlr3'. It offers various optimization methods e.g. grid search, random search and generalized simulated annealing. …

r-bdgraph 2.65

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 2.10.0

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

r-beanplot 1.3.1

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

r-beclear 2.10.0

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict…

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 0.4.0

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-benchmarkme 1.0.7

This package provides functionality to benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version. …

r-benchmarkmedata 1.0.4

This package contains the data set for the crowd-sourced benchmarks from running the `benchmarkme' package. …

r-bezier 1.1.2

This package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting. …

r-bgeecall 1.10.0

BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of…

r-bgeedb 2.20.1

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns. …

r-bgmix 1.54.0

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

r-bgx 1.60.0

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

r-bh 1.78.0-0

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

r-bhc 1.46.0

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 0.4.2.3

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

r-bicare 1.52.0

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

r-biclust 2.0.3

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-bien 1.2.5

This package provides tools for accessing the Botanical Information and Ecology Network (BIEN) database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data. …

r-bifet 1.14.0

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 1.30.0

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 1.20.0

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. …

r-bigmemoryextras 1.38.0

This package defines a `BigMatrix' `ReferenceClass' which adds safety and convenience features to the `filebacked.big.matrix' class from the `bigmemory' package. `BigMatrix' protects against segfaults by monitoring and gracefully restoring the connection to…

r-bigpint 1.10.0

This package provides methods for visualizing large multivariate datasets using static and interactive scatterplot matrices, parallel coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially…

r-bigrquery 1.4.0

This package provides an R interface to Google's BigQuery database. …

r-billboarder 0.3.1

This package provides an `htmlwidgets' interface to billboard.js, a re-usable easy interface JavaScript chart library, based on D3 v4+. Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and…

r-bindr 0.1.1

This package provides a simple interface for creating active bindings where the bound function accepts additional arguments. …

r-bindrcpp 0.2.2

This package provides an easy way to fill an environment with active bindings that call a C++ function. …

r-binman 0.1.2

This package provides tools and functions for managing the download of binary files. Binary repositories are defined in the YAML format. Defining new pre-download, download and post-download templates allow additional…

r-binom 1.1-1

Constructs confidence intervals on the probability of success in a binomial experiment via several parameterizations …

r-bio3d 2.4-3

This package provides utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence…

r-bioassayr 1.32.1

bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses…

r-biobase 2.54.0

This package provides functions that are needed by many other packages on Bioconductor or which replace R functions. …

r-biobroom 1.26.0

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to `tidy' data. It thus serves as a complement to the `broom'…

r-biobtreer 1.6.0

The biobtreeR package provides an interface to biobtree, a tool which covers large sets of bioinformatics datasets and allows search and chain mappings functionalities. …

r-bioccasestudies 1.52.0

This package provides software and data to support the case studies monograph. …

r-bioccheck 1.30.0

This package contains tools to perform additional quality checks on R packages that are to be submitted to the Bioconductor repository. …

r-biocdockermanager 1.6.0

This package works analogous to BiocManager but for Docker images. Use the BiocDockerManager package to install and manage Docker images provided by the Bioconductor project. …

r-biocfilecache 2.2.1

This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly…

r-biocgenerics 0.40.0

This package provides S4 generic functions needed by many Bioconductor packages. …

r-biocgraph 1.56.0

This package provides examples and code that make use of the different graph related packages produced by Bioconductor. …

r-biocio 1.4.0

This package implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard…

r-biocmanager 1.30.16

This package provides a convenient tool to install and update Bioconductor packages. …

r-biocneighbors 1.12.0

This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented…

r-bioconcotk 1.14.0

The purpose of this package is to provide a central interface to various tools for genome-scale analysis of cancer studies. …

r-biocor 1.18.0

This package provides tools to calculate functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets,…

r-biocparallel 1.28.3

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects. …

r-biocpkgtools 1.12.2

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is…

r-biocset 1.8.1

BiocSet displays different biological sets in a triple tibble format. These three tibbles are `element', `set', and `elementset'. The user has the ability to activate one of these three tibbles…

r-biocsingular 1.10.0

This package implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible,…

r-biocstyle 2.22.0

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality. …

r-biocthis 1.4.0

This package expands the `usethis' package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly. …

r-biocversion 3.14.0

This package provides repository information for the appropriate version of Bioconductor. …

r-biocviews 1.62.1

The purpose of biocViews is to create HTML pages that categorize packages in a Bioconductor package repository according to keywords, also known as views, in a controlled vocabulary. …

r-biocworkflowtools 1.20.0

This package provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow. …

r-biodb 1.2.2

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access…

r-biodist 1.66.0

This package provides a collection of software tools for calculating distance measures. …

r-biomart 2.50.3

biomaRt provides an interface to a growing collection of databases implementing the http://www.biomart.org (BioMart software suite). The package enables retrieval of large amounts of data in a uniform way without the…

r-biomformat 1.22.0

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is…

r-biomvcclass 1.62.0

This package contains classes used in model-view-controller (MVC) design. …

r-biomvrcns 1.34.0

In this package, a "Hidden Semi Markov Model" (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high…

r-bionero 1.2.0

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer…

r-bionet 1.54.0

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests…

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