Packages — R (Page 2 of 11)

r-bsgenome 1.50.0 — 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.

r-bsgenome-mmusculus-ucsc-mm10 1.4.0 — Full genome sequences for Mouse

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 — Full genome sequences for Mouse

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 — Full masked genome sequences for Mouse

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, 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-cairo 1.5-9 — R graphics device using Cairo graphics library

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). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.

r-calibrate 1.7.2 — Calibration of scatterplot and biplot axes

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

r-callr 3.0.0 — Call R from R

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

r-car 3.0-2 — Companion to applied regression

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

r-cardata 3.0-2 — Data Sets for the book Companion to Applied Regression

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

r-caret 6.0-80 — Classification and regression training

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

r-catdap 1.3.4 — Tools for categorical data analysis

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 (AIC).

r-category 2.48.0 — Category analysis

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

r-catools 1.17.1.1 — Various tools including functions for moving window statistics

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, etc.

r-catterplots 0-2.40063ec57 — Scatter plots with cat shaped points

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

r-cellranger 1.1.0 — Translate spreadsheet cell ranges to rows and columns

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

r-centipede 1.2 — Predict transcription factor binding sites

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 then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

r-cgdsr 1.2.10 — R-based API for accessing the MSKCC Cancer Genomics Data Server

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 1.42.0 — Base functions and classes for arrayCGH data analysis

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

r-cghcall 2.44.0 — Base functions and classes for arrayCGH data analysis

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

r-checkmate 1.8.5 — Fast and versatile argument checks

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-chipcomp 1.12.0 — Quantitative comparison of multiple ChIP-seq datasets

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.

r-chipexoqual 1.6.0 — Quality control pipeline for ChIP-exo/nexus data

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.

r-chipkernels 1.1-1.c9cfcacb6 — Build string kernels for DNA Sequence analysis

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

r-chippeakanno 3.16.0 — Peaks annotation from ChIP-seq and ChIP-chip experiments

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).

r-chipseq 1.32.0 — Package for analyzing ChIPseq data

This package provides tools for processing short read data from ChIPseq experiments.

r-chron 2.3-53 — Chronological R objects which can handle dates and times

This package provides chronological R objects which can handle dates and times.

r-circlize 0.4.4 — Circular visualization

Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.

r-circular 0.4-93 — Circular statistics

This package provides tools for circular statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

r-circus 0.1.5 — Annotation, analysis and visualization of circRNA data

Circus is an R package for annotation, analysis and visualization of circRNA data. Users can annotate their circRNA candidates with host genes, gene featrues they are spliced from, and discriminate between known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs can be calculated, and a number of descriptive plots easily generated.

r-class 7.3-14 — R functions for classification

This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

r-cli 1.0.1 — Helpers for developing command line interfaces

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.

r-clipr 0.4.1 — Read and write from the system clipboard

This package provides simple utility functions to read from and write to the system clipboards.

r-clisymbols 1.2.0 — Unicode symbols at the R prompt

This package provides a small subset of Unicode symbols, that are useful when building command line applications. They fall back to alternatives on terminals that do not support Unicode.

r-cluster 2.0.7-1 — Methods for cluster analysis

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

r-clusteval 0.1 — Evaluation of clustering algorithms

This R package provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.

r-coda 0.19-2 — This is a package for Output Analysis and Diagnostics for MCMC

This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

r-codedepends 0.6.5 — Analysis of R code for reproducible research and code comprehension

This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.

r-codetools 0.2-15 — Code analysis tools for R

This package provides code analysis tools for R to check R code for possible problems.

r-coin 1.2-2 — Conditional inference procedures in a permutation test framework

This package provides conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.

r-colorout 1.2-0 — Colorize output in the R REPL

colorout is an R package that colorizes R output when running in terminal emulator.

R STDOUT is parsed and numbers, negative numbers, dates in the standard format, strings, and R constants are identified and wrapped by special ANSI scape codes that are interpreted by terminal emulators as commands to colorize the output. R STDERR is also parsed to identify the expressions warning and error and their translations to many languages. If these expressions are found, the output is colorized accordingly; otherwise, it is colorized as STDERROR (blue, by default).

You can customize the colors according to your taste, guided by the color table made by the command show256Colors(). You can also set the colors to any arbitrary string. In this case, it is up to you to set valid values.

r-colorspace 1.3-2 — Color space manipulation

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

r-commonmark 1.6 — CommonMark and Github Markdown Rendering in R

The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including HTML, LaTeX and groff man. In addition, it exposes the markdown parse tree in XML format. The latest version of this package also adds support for Github extensions including tables, autolinks and strikethrough text.

r-compare 0.2-6 — Comparing objects for differences

This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.

r-complexheatmap 1.20.0 — Making Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

r-complexplus 2.1 — Functions of complex or real variables

This package extends several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.

r-compquadform 1.4.3 — Distribution function of quadratic forms in normal variables

This package provides functions to compute the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.

r-copyhelper 1.6.0 — Helper files for CopywriteR

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.

r-copynumber 1.22.0 — Segmentation of single- and multi-track copy number data

This package segments single- and multi-track copy number data by a penalized least squares regression method.

r-copywriter 2.14.0 — Copy number information from targeted sequencing

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

r-corrplot 0.84 — Visualization of a correlation matrix

This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.

r-cowplot 0.9.3 — Streamlined plot theme and plot annotations for ggplot2

This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications.

r-crayon 1.3.4 — Colored terminal output for R

Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the "chalk" JavaScript project.

r-crosstalk 1.0.0 — Inter-widget interactivity for HTML widgets

This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). It currently supports linked brushing and filtering.

r-cssam 1.4-1.9ec58c9 — Cell type-specific statistical analysis of microarray

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

r-ctc 1.56.0 — Cluster and tree conversion

This package provides tools for exporting and importing classification trees and clusters to other programs.

r-cubature 1.4-1 — Adaptive multivariate integration over hypercubes

This package is an R wrapper around the cubature C library for adaptive multivariate integration over hypercubes. This version provides both hcubature and pcubature routines in addition to a vector interface.

r-curl 3.2 — HTTP client for R

The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption, gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.

r-cvst 0.2-2 — Fast cross-validation via sequential testing

This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

r-data-table 1.11.8 — Enhanced version of data.frame R object

The R package data.table is an extension of data.frame providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.

r-dbi 1.0.0 — R database interface

The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

r-dbplyr 1.2.2 — Dplyr back end for databases

This package provides a dplyr back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a DBI back end; more advanced features require SQL translation to be provided by the package author.

r-ddalpha 1.3.4 — Depth-Based classification and calculation of data depth

This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.

r-debugme 1.1.0 — Debug R packages

This package allows the user to specify debug messages as special string constants, and control debugging of packages via environment variables.

r-delayedarray 0.8.0 — Delayed operations on array-like objects

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.

r-delayedmatrixstats 1.4.0 — Functions that apply to rows and columns of DelayedMatrix objects

This package provides a port of the matrixStats API for use with DelayedMatrix objects from the DelayedArray package. It contains high-performing functions operating on rows and columns of DelayedMatrix objects, e.g. colMedians, rowMedians, colRanks, rowRanks, colSds, and rowSds. Functions are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

r-dendextend 1.9.0 — Extending 'dendrogram' functionality in R

This package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.

r-deoptimr 1.0-8 — Differential evolution optimization in pure R

This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language.

r-desc 1.2.0 — Manipulate DESCRIPTION Files

This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.

r-deseq 1.34.0 — Differential gene expression analysis

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

r-deseq2 1.22.1 — Differential gene expression analysis

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

r-desolve 1.21 — Solvers for initial value problems of differential equations

This package provides functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations. The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps. The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.

r-destiny 2.12.0 — Create and plot diffusion maps

This package provides tools to create and plot diffusion maps.

r-devtools 2.0.1 — Tools to make developing R packages easier

The devtools package is a collection of package development tools to simplify the devolpment of R packages.

r-dexseq 1.28.0 — Inference of differential exon usage in RNA-Seq

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

r-dichromat 2.0-0 — Color schemes for dichromats

Dichromat collapses red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

r-diffbind 2.10.0 — Differential binding analysis of ChIP-Seq peak data

This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

r-diffusionmap 1.1-0.1 — Diffusion map

This package implements the diffusion map method of data parametrization, including creation and visualization of diffusion maps, clustering with diffusion K-means and regression using the adaptive regression model.

r-digest 0.6.18 — Create cryptographic hash digests of R objects

This package contains an implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code.

Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

r-dimred 0.2.2 — Framework for dimensionality reduction

This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.

r-diptest 0.75-7 — Hartigan's dip test statistic for unimodality

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.

r-directlabels 2018.05.22 — Direct labels for multicolor plots

This package provides an extensible framework for automatically placing direct labels onto multicolor plots. Label positions are described using positioning methods that can be re-used across several different plots. There are heuristics for examining trellis and ggplot objects and inferring an appropriate positioning method.

r-dirichletmultinomial 1.24.0 — Dirichlet-Multinomial mixture models for microbiome data

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

r-distillery 1.0-4 — Functions for confidence intervals and object information

This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.

r-diversitree 0.9-10 — Comparative 'phylogenetic' analyses of diversification

This package contains a number of comparative "phylogenetic" methods, mostly focusing on analysing diversification and character evolution. Contains implementations of "BiSSE" (Binary State Speciation and Extinction) and its unresolved tree extensions, "MuSSE" (Multiple State Speciation and Extinction), "QuaSSE", "GeoSSE", and "BiSSE-ness" Other included methods include Markov models of discrete and continuous trait evolution and constant rate speciation and extinction.

r-dnabarcodes 1.12.0 — Create and analyze DNA barcodes

This package offers tools to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.

r-dnacopy 1.56.0 — Implementation of a circular binary segmentation algorithm

This package implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

r-doby 4.6-2 — Groupwise statistics, LSmeans, linear contrasts, and utilities

This package contains:

  • facilities for working with grouped data: do something to data stratified by some variables.

  • implementations of least-squares means, general linear contrasts, and

  • miscellaneous other utilities.

r-domc 1.3.5 — Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

r-doparallel 1.0.14 — Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the parallel package.

r-dosnow 1.0.16 — Foreach parallel adaptor for the snow package

This package provides a parallel backend for the %dopar% function using the snow package.

r-dplyr 0.7.8 — Tools for working with data frames in R

dplyr is the next iteration of plyr. It is focussed on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.

r-dropbead 0-2.d746c6f — Basic exploration and analysis of Drop-seq data

This package offers a quick and straight-forward way to explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.