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Packages — R (Page 3 of 35)

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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 1.8.0

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 1.24.0

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 1.14.0

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 1.36.0

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 1.4.0

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 1.3.2

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 2.4-1

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 1.26.0

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 2.48.0

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

r-biobroom 1.20.0

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-bioccasestudies 1.50.0

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

r-bioccheck 1.24.0

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

r-biocfilecache 1.12.1

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 0.34.0

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

r-biocgraph 1.50.0

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

r-biocmanager 1.30.10

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

r-biocneighbors 1.6.0

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 1.8.0

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

r-biocor 1.12.0

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 1.22.0

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

r-biocpkgtools 1.6.0

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 1.2.2

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 1.4.0

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 2.16.1

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

r-biocversion 3.11.1

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

r-biocviews 1.56.2

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 1.14.0

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

r-biodist 1.60.0

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

r-biomart 2.44.1

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-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 1.16.0

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 2.56.0

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-biovizbase 1.36.0

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 3.20.0

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-bisquerna 1.0.4

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 1.0-6

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

r-blme 1.0-4

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 1.2.1

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 1.6

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 1.0.0

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-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 0.20

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

r-boot 1.3-25

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…

r-boruta 7.0.0

This package provides an all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies (shadows). …

r-bqtl 1.0-32

This is a QTL mapping toolkit for inbred crosses and recombinant inbred lines. It includes maximum likelihood and Bayesian tools. …

r-brew 1.0-6

The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's…

r-brglm 0.6.2

Fit generalized linear models with binomial responses using either an adjusted-score approach to bias reduction or maximum penalized likelihood where penalization is by Jeffreys invariant prior. These procedures return estimates with improved…

r-bridgesampling 1.0-0

This package provides functions for estimating marginal likelihoods, Bayes factors, posterior model probabilities, and normalizing constants in general, via different versions of bridge sampling. …

r-brms 2.13.5

Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others --…

r-brobdingnag 1.2-6

This package handles very large numbers in R. Real numbers are held using their natural logarithms, plus a logical flag indicating sign. The package includes a vignette that gives a…

r-broom 0.7.1

This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like `dplyr', `tidyr'…

r-bseqsc 1.0-1.fef3f3e

BSeq-sc is a bioinformatics analysis pipeline that leverages single-cell sequencing data to estimate cell type proportion and cell type-specific gene expression differences from RNA-seq data from bulk tissue samples. This is…

r-bsgenome 1.56.0

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation. …

r-bsgenome-celegans-ucsc-ce10 1.4.0

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings objects. …

r-bsgenome-celegans-ucsc-ce6 1.4.0

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects. …

r-bsgenome-dmelanogaster-ucsc-dm3 1.4.0

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. …

r-bsgenome-dmelanogaster-ucsc-dm3-masked 1.3.99

This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except…

r-bsgenome-dmelanogaster-ucsc-dm6 1.4.1

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings objects. …

r-bsgenome-hsapiens-1000genomes-hs37d5 0.99.1

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37. …

r-bsgenome-hsapiens-ncbi-grch38 1.3.1000

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. …

r-bsgenome-hsapiens-ucsc-hg19 1.4.0

This package provides full genome sequences for Homo sapiens as provided by UCSC (hg19, February 2009) and stored in Biostrings objects. …

r-bsgenome-hsapiens-ucsc-hg19-masked 1.3.99

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19,…

r-bsgenome-hsapiens-ucsc-hg38 1.4.1

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm10 1.4.0

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm9 1.4.0

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects. …

r-bsgenome-mmusculus-ucsc-mm9-masked 1.3.99

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9,…

r-bumphunter 1.30.0

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies. …

r-cairo 1.5-12.2

This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). …

r-calculus 0.2.1

Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion,…

r-calibrate 1.7.7

This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots. …

r-callr 3.4.4

It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This package does exactly that. …

r-capushe 1.1.1

This package provides tools for the calibration of penalized criteria for model selection. The calibration methods available are based on the slope heuristics. …

r-car 3.0-10

This package provides functions and datasets from book Companion to Applied regression, Second Edition, Sage, 2011. …

r-cardata 3.0-4

This package provides datasets to accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage. …

r-caret 6.0-86

This package provides miscellaneous functions for training and plotting classification and regression models. …

r-catdap 1.3.5

This package provides functions for analyzing multivariate data. Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the "Akaike Information Criterion"…

r-category 2.54.0

This package provides a collection of tools for performing category analysis. …

r-catools 1.18.0

This package contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum,…

r-catterplots 0-3.ae17cd5

Did you ever wish you could make scatter plots with cat shaped points? Now you can! …

r-cdm 7.5-15

This package provides functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. It enables the estimation of the DINA and DINO model, the multiple group…

r-cellranger 1.1.0

This package provides helper functions to work with spreadsheets and the `A1:D10' style of cell range specification. …

r-centipede 1.2

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and…

r-cgdsr 1.3.0

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). …

r-cghbase 1.48.0

This package contains functions and classes that are needed by the `arrayCGH' packages. …

r-cghcall 2.50.0

This package contains functions and classes that are needed by `arrayCGH' packages. …

r-checkmate 2.0.0

This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead. …

r-chemminer 3.40.0

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and…

r-chemometricswithr 0.1.13

This package provides functions and scripts used in the book "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences" by Ron Wehrens, Springer (2011). …

r-chipcomp 1.18.0

ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets. …

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