Packages — R (Page 3 of 52)

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r-bayesfactor 0.9.12-4.2

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 1.8.1

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 0.11.5

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 1.11

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 0.4.0

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 2.64

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 1.2

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 2.20.0

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 1.75.0-0

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 1.2.4

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-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-bio3d 2.4-2

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 1.32.0

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 2.2.0

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 1.28.1

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 1.2.1

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 2.50.1

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…

r-bionetstat 1.14.0

This package provides a package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view. …

r-bioqc 1.22.0

BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that…

r-bios2cor 2.2

This package provides utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a…

r-biosigner 1.22.0

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to…

r-biostrings 2.62.0

This package provides memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. …

r-biotip 1.8.0

This package adopts tipping-point theory to transcriptome profiles to help unravel disease regulatory trajectory. …

r-biotmle 1.18.0

This package provides tools for differential expression biomarker discovery based on microarray and next-generation sequencing data that leverage efficient semiparametric estimators of the average treatment effect for variable importance analysis. Estimation and…

r-biovizbase 1.42.0

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization.…

r-birewire 3.26.0

This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the…

r-birta 1.31.0

Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. "birta" (Bayesian Inference of Regulation of Transcriptional Activity) uses the…

r-biscuiteer 1.8.0

This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age…

r-biscuiteerdata 1.6.0

This package contains default datasets used by the Bioconductor package biscuiteer. …

r-bisquerna 1.0.5

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate…

r-bit 4.0.4

This package provides bitmapped vectors of booleans (no `NA's), coercion from and to logicals, integers and integer subscripts, fast boolean operators and fast summary statistics. With `bit' class vectors of true…

r-bit64 4.0.5

The bit64 package provides serializable S3 atomic 64 bit (signed) integers that can be used in vectors, matrices, arrays and `data.frames'. Methods are available for coercion from and to logicals, integers,…

r-bitops 1.0-7

This package provides functions for bitwise operations on integer vectors. …

r-blme 1.0-5

This package provides tools for maximum a posteriori estimation for linear and generalized linear mixed-effects models in a Bayesian setting. It extends the lme4 package. …

r-blob 1.2.2

Raw vectors in R are useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides…

r-blockfest 2.0

This package provides an R implementation of an extension of the BayeScan software for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this…

r-blockmodeling 1.0.5

This package is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be…

r-bluster 1.4.0

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering…

r-bmp 0.3

This package provides pure R tools to read BMP format images. It is currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images. …

r-boa 1.1.8-2

This package provides a menu-driven program and library of functions for carrying out convergence diagnostics and statistical and graphical analysis of "Markov chain Monte Carlo" (MCMC) sampling output. …

r-bookdown 0.24

This package provides output formats and utilities for authoring books and technical documents with R Markdown. …

r-boot 1.3-28

This package provides functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A.C. Davison and D.V. Hinkley (1997, CUP), originally written by Angelo Canty for…

r-bootstrap 2019.6

This package provides software and data for the book "An Introduction to the Bootstrap" by B. Efron and R. Tibshirani, 1993, Chapman and Hall. This package is primarily provided…

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