Packages — R (Page 1 of 11)

r 3.5.0 — Environment for statistical computing and graphics

This is a GNU package.

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.

r-a3 1.0.0 — Error metrics for predictive models

This package supplies tools for tabulating and analyzing the results of predictive models. The methods employed are applicable to virtually any predictive model and make comparisons between different methodologies straightforward.

r-abbyyr 0.5.4 — Access to Abbyy Optical Character Recognition (OCR) API

This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see

r-abc 2.1 — Tools for Approximate Bayesian Computation (ABC)

This package implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.

r-abc-data 1.0 — Data for Approximate Bayesian Computation (ABC) package

This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

r-abcanalysis 1.2.1 — Computed ABC Analysis

Multivariate data sets often differ in several factors or derived statistical parameters, which have to be selected for a valid interpretation. Basing this selection on traditional statistical limits leads occasionally to the perception of losing information from a data set. This package provides tools to calculate these limits on the basis of the mathematical properties of the distribution of the analyzed items.

r-abcoptim 0.15.0 — Optimization of Artificial Bee Colony algorithm

Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE) algorithms, and uses only common control parameters such as colony size and maximum cycle number. The r-abcoptim implements the Artificial bee colony optimization algorithm This version is a work-in-progress and is written in R code.

r-abcp2 1.2 — Approximate Bayesian Computational Model for Estimating P2

This package tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.

r-abcrf 1.7.1 — Approximate bayesian computation via random forests

This package performs approximate bayesian computation (ABC) model choice and parameter inference via random forests. This machine learning tool named random forests (RF) can conduct selection among the highly complex models covered by ABC algorithms.

r-abctools 1.1.3 — Tools for ABC analyses

This r-abctools package provides tools for approximate Bayesian computation including summary statistic selection and assessing coverage. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold.

r-abd 0.2-8 — Analysis of biological data

The r-abd package contains data sets and sample code for the Analysis of biological data by Michael Whitlock and Dolph Schluter.

r-abe 3.0.1 — Augmented backward elimination

This package performs augmented backward elimination and checks the stability of the obtained model. Augmented backward elimination combines significance or information based criteria with the change in estimate to either select the optimal model for prediction purposes or to serve as a tool to obtain a practically sound, highly interpretable model.

r-abf2 0.7-1 — Load gap-free axon r-abf2 files

This package loads electrophysiology data from ABF2 files, as created by Axon Instruments/Molecular Devices software. Only files recorded in gap-free mode are currently supported.

r-abhgenotyper 1.0.1 — Visualize and manipulate ABH genotypes

The r-abhgenotyper package provides simple imputation, error-correction and plotting capacities for genotype data. The package is supposed to serve as an intermediate but independent analysis tool between the TASSEL GBS pipeline and the r-qtl package. It provides functionalities not found in either TASSEL or r-qtl in addition to visualization of genotypes as "graphical genotypes".

r-abind 1.4-5 — Combine multidimensional arrays

This package provides tools to combine multidimensional arrays into a single array. This is a generalization of cbind and rbind. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions adrop, asub, and afill for manipulating, extracting and replacing data in arrays.

r-abjutils 0.2.1 — Collection of tools for jurimetrical analysis

This package implements general purpose tools, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.

r-abnormality 0.1.0 — Measure a subject's abnormality with respect to a reference population

This package contains functions to implement the methodology and considerations laid out by Marks et al. in the article "Measuring abnormality in high dimensional spaces: applications in biomechanical gait analysis". Using high-dimensional datasets to measure a subject's overall level of abnormality as compared to a reference population is often needed in outcomes research.

r-abodoutlier 0.1 — Angle-based outlier detection

This package performs angle-based outlier detection on a given data frame. It offers three methods to process data:

  1. full but slow implementation using all the data that has cubic complexity;

  2. a fully randomized method;

  3. a method using k-nearest neighbours.

These algorithms are well suited for high dimensional data outlier detection.

r-abps 0.2 — Abnormal blood profile score to detect blood doping

This package offers an implementation of the Abnormal blood profile score (ABPS). The ABPS is a part of the Athlete biological passport program of the World anti-doping agency, which combines several blood parameters into a single score in order to detect blood doping. The package also contains functions to calculate other scores used in anti-doping programs, such as the ratio of hemoglobin to reticulocytes (OFF-score), as well as example data.

r-absfiltergsea 1.5.1 — Improved false positive control of gene-permuting with absolute filtering

This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

r-absim 0.2.6 — Time resolved simulations of antibody repertoires

This package provides simulation methods for the evolution of antibody repertoires. The heavy and light chain variable region of both human and C57BL/6 mice can be simulated in a time-dependent fashion. Both single lineages using one set of V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins with an initial V-D-J recombination event, starting the first phylogenetic tree. Upon completion, the main loop of the algorithm begins, with each iteration representing one simulated time step. Various mutation events are possible at each time step, contributing to a diverse final repertoire.

r-abundant 1.1 — Abundant regression and high-dimensional principal fitted components

This package provides tools to fit and predict with the high-dimensional principal fitted components model. This model is described by Cook, Forzani, and Rothman (2012) doi:10.1214/11-AOS962.

r-ac3net 1.2.2 — Inferring directional conservative causal core gene networks

This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.

r-aca 1.1 — Abrupt change-point or aberration detection in point series

This package offers an interactive function for the detection of breakpoints in series.

r-acc 1.3.3 — Exploring accelerometer data

This package processes accelerometer data from uni-axial and tri-axial devices and generates data summaries. Also, includes functions to plot, analyze, and simulate accelerometer data.

r-accelerometry 3.1.2 — Functions for processing accelerometer data

This package provides a collection of functions that perform operations on time-series accelerometer data, such as identify the non-wear time, flag minutes that are part of an activity bout, and find the maximum 10-minute average count value. The functions are generally very flexible, allowing for a variety of algorithms to be implemented.

r-accelmissing 1.4 — Missing value imputation for accelerometer data

This package provides a statistical method to impute the missing values in accelerometer data. The methodology includes both parametric and semi-parametric multiple imputations under the zero-inflated Poisson lognormal model. It also provides multiple functions to preprocess the accelerometer data previous to the missing data imputation. These include detecting the wearing and the non-wearing time, selecting valid days and subjects, and creating plots.

r-acceptancesampling 1.0-5 — Creation and evaluation of acceptance sampling plans

This r-acceptancesampling provides functionality for creating and evaluating acceptance sampling plans. Acceptance sampling is a methodology commonly used in quality control and improvement. International standards of acceptance sampling provide sampling plans for specific circumstances. The aim of this package is to provide an easy-to-use interface to visualize single, double or multiple sampling plans. In addition, methods have been provided to enable the user to assess sampling plans against pre-specified levels of performance, as measured by the probability of acceptance for a given level of quality in the lot.

r-acclma 1.0 — ACC & LMA graph plotting

This package contains a function that imports data from a CSV file, or uses manually entered data from the format (x, y, weight) and plots the appropriate ACC vs LOI graph and LMA graph. The main function is plotLMA (source file, header) that takes a data set and plots the appropriate LMA and ACC graphs. If no source file (a string) was passed, a manual data entry window is opened. The header parameter indicates by TRUE/FALSE (false by default) if the source CSV file has a header row or not. The dataset should contain only one independent variable (x) and one dependent variable (y) and can contain a weight for each observation.

r-acepack 1.4.1 — Functions for regression transformations

This package provides ACE and AVAS methods for choosing regression transformations.

r-acsnminer — Gene enrichment analysis

This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.

r-adaptivesparsity 1.6 — Adaptive sparsity models

This package implements the Figueiredo machine learning algorithm for adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models.

r-ade4 1.7-13 — Multivariate data analysis and graphical display

The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods.

r-affy 1.58.0 — Methods for affymetrix oligonucleotide arrays

This package contains functions for exploratory oligonucleotide array analysis.

r-affyio 1.50.0 — Tools for parsing Affymetrix data files

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-algdesign 1.1-7.3 — Algorithmic experimental design

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 blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.

r-amap 0.8-16 — Another multidimensional analysis package

This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions).

r-analytics 2.0 — Collection of data analysis tools

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 for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.

r-annotate 1.58.0 — Annotation for microarrays

This package provides R environments for the annotation of microarrays.

r-annotationdbi 1.42.1 — Annotation database interface

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

r-annotationfilter 1.4.0 — Facilities for filtering Bioconductor annotation resources

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 1.22.2 — Code for building annotation database packages

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

r-annotationhub 2.12.1 — Client to access AnnotationHub resources

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 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

r-ape 5.1 — Analyses of phylogenetics and evolution

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, and several other tools.

r-argparse 1.1.1 — Command line optional and positional argument parser

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 0.4 — Command-line argument parser

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 executable script.

r-aroma-light 3.10.0 — Methods for normalization and visualization of microarray data

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 be wrapped up in higher-level classes.

r-arules 1.6-1 — Mining association rules and frequent itemsets

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-aspi 0.2.0 — Analysis of symmetry of parasitic infections

This package provides tools for the analysis and visualization of bilateral asymmetry in parasitic infections.

r-assertthat 0.2.0 — Easy pre and post assertions

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 know what they've done wrong.

r-auc 0.3.0 — Compute the area under the curve of selected measures

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 accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.

r-backports 1.1.2 — Reimplementations of functions introduced since R 3.0.0

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 (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.

r-bamsignals 1.12.1 — Extract read count signals from bam files

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. It also handles paired-end data.

r-base64 2.0 — Base64 encoder and decoder

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 — Tools for Base64 encoding

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

r-basix 1.1 — Efficient C/C++ toolset for R

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

r-batchjobs 1.7 — Batch computing with R

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-bayesplot 1.6.0 — Plotting for Bayesian models

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 functions that can be easily used by developers working on a variety of R packages for Bayesian modeling.

r-bayseq 2.14.0 — Bayesian analysis of differential expression patterns in count data

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 — Miscellaneous functions for R package development

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

r-bbmle 1.0.20 — Tools for General Maximum Likelihood Estimation

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-beachmat 1.2.1 — Compiling Bioconductor to handle each matrix type

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

r-beeswarm 0.2.3 — Implementation of bee swarm plots

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-bh 1.66.0-1 — R package providing subset of Boost headers

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

r-biased-urn 1.07 — Biased urn model distributions

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 — Biased Urn model distributions

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 — Bibtex parser

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

r-bigmemory 4.5.33 — Manage large matrices with shared memory or memory-mapped files

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 — Shared resource interface for the bigmemory package

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

r-bindr 0.1.1 — Parametrized active bindings

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

r-bindrcpp 0.2.2 — Rcpp interface to active bindings

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

r-biobase 2.40.0 — Base functions for Bioconductor

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

r-bioccheck 1.16.0 — Executes Bioconductor-specific package checks

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

r-biocgenerics 0.26.0 — S4 generic functions for Bioconductor

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

r-biocinstaller 1.30.0 — Install Bioconductor packages

This package is used to install and update R packages from Bioconductor, CRAN, and Github.

r-biocparallel 1.14.2 — Bioconductor facilities for parallel evaluation

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

r-biocstyle 2.8.2 — Bioconductor formatting styles

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

r-biocviews 1.48.3 — Bioconductor package categorization helper

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-biomart 2.36.1 — Interface to BioMart databases

biomaRt provides an interface to a growing collection of databases implementing the The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

r-biostrings 2.48.0 — String objects and algorithms for biological sequences

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 1.28.2 — Basic graphic utilities for visualization of genomic data

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. This saves development effort and encourages consistency.

r-bit 1.1-14 — Class for vectors of 1-bit booleans

This package provides bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts, fast boolean operators and fast summary statistics. With bit class vectors of true binary booleans, TRUE and FALSE can be stored with 1 bit only.

r-bit64 0.9-7 — S3 class for vectors of 64 bit integers

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, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as match and order support interactive data exploration and manipulation and optionally leverage caching.

r-bitops 1.0-6 — Bitwise operations

This package provides functions for bitwise operations on integer vectors.

r-blob 1.1.1 — Simple S3 Class for representing vectors of binary data

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 the blob object, a list of raw vectors, suitable for use as a column in data frame.

r-blockfest 1.6 — Bayesian calculation of region-specific fixation index

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 new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.

r-bookdown 0.7 — Authoring books and technical documents with R markdown

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

r-boot 1.3-20 — Bootstrap functions for R

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 S.

r-brew 1.0-6 — Templating framework for report generation

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 psp module.

r-broom 0.5.0 — Convert statistical analysis objects into tidy data frames

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 and ggplot2. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.

r-bseqsc 1.0-1.fef3f3e — Deconvolution of bulk sequencing experiments using single cell data

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 a companion package to the publication "A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure." Baron et al. Cell Systems (2016)

r-bsgenome 1.48.0 — Infrastructure for Biostrings-based genome data packages

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 — Full genome sequences for Worm

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 — Full genome sequences for Worm

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 — Full genome sequences for Fly

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 — Full masked genome sequences for Fly

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 that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-bsgenome-dmelanogaster-ucsc-dm6 1.4.1 — Full genome sequences for Fly

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 — Full genome sequences for Homo sapiens

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

r-bsgenome-hsapiens-ucsc-hg19 1.4.0 — Full genome sequences for Homo sapiens

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 — Full masked genome sequences for Homo sapiens

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, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.