Packages — R (Page 6 of 39)

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r-feature 1.2.14

The feature package contains functions to display and compute kernel density estimates, significant gradient and significant curvature regions. Significant gradient and/or curvature regions often correspond to significant features (e.g. local modes). …

r-ff 4.0.4

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory. …

r-ffbase 0.13.1

This package extends the out of memory vectors of `ff' with statistical functions and other utilities to ease their usage. …

r-fftwtools 0.9-9

This package provides a wrapper for several FFTW functions. It provides access to the two-dimensional FFT, the multivariate FFT, and the one-dimensional real to complex FFT using the FFTW3 library. …

r-fgsea 1.16.0

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to…

r-fgui 1.0-8

Rapidly create a GUI for a function you created by automatically creating widgets for arguments of the function. This package automatically parses help routines for context-sensitive help to these arguments. …

r-fhtest 1.5

This package provides functions to compare two or more survival curves with: * The Fleming-Harrington test for right-censored data based on permutations and on…

r-fields 11.6

This is a package for curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and…

r-filematrix 1.3

This package provides an interface for working with large matrices stored in files, not in computer memory. It supports multiple non-character data types (double, integer, logical and raw) of various sizes…

r-findpython 1.0.5

This package was designed to find an acceptable Python binary that matches version and feature constraints. …

r-fit-models 0.64

The `fit.models' function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the `robust' package to compare robustly and classically fitted model objects. The aim of the…

r-fitdistrplus 1.1-3

This package extends the `fitdistr' function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored,…

r-fithic 1.16.0

Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C. …

r-fivethirtyeight 0.1.0

This R package provides access to the code and data sets published by the statistics blog FiveThirtyEight. …

r-flare 1.7.0

This package provides implementations of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear models. …

r-flashclust 1.01-2

This package provides a fast implementation of hierarchical clustering. …

r-flexclust 1.4-0

The main function `kcca' implements a general framework for k-centroids cluster analysis supporting arbitrary distance measures and centroid computation. Further cluster methods include hard competitive learning, neural gas, and QT clustering. There…

r-flexdashboard 0.5.2

This package provides an R Markdown format for converting an R Markdown document to a grid-oriented dashboard. The dashboard flexibly adapts the size of its components to the containing web page. …

r-flexmix 2.3-17

This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by…

r-flexsurv 1.1.1

This package provides flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R…

r-flextable 0.6.1

This package provides tools to create pretty tables for HTML documents and other formats. Functions are provided to let users create tables, modify and format their content. It extends the…

r-flock 0.7

This package implements synchronization between R processes (spawned by using the `parallel' package for instance) using file locks. It supports both exclusive and shared locking. …

r-flowclust 3.28.0

This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation. …

r-flowcore 2.2.0

This package provides S4 data structures and basic functions to deal with flow cytometry data. …

r-flowmeans 1.50.0

This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. …

r-flowsom 1.22.0

FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees. …

r-flowstats 4.2.0

This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the `flowCore' package. …

r-flowutils 1.54.0

This package provides utilities for flow cytometry data. …

r-flowviz 1.54.0

This package provides visualization tools for flow cytometry data. …

r-flowworkspace 4.2.0

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the…

r-fmsb 0.7.0

This package provides several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related…

r-fnn 1.1.3

This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms. Related applications including KNN classification, regression and information measures are implemented. …

r-forcats 0.5.0

This package provides helpers for reordering factor levels (including moving specified levels to front, ordering by first appearance, reversing, and randomly shuffling), and tools for modifying factor levels (including collapsing rare levels into…

r-foreach 1.5.1

This package provides support for the `foreach' looping construct. `foreach' is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. …

r-forecast 8.13

This package provides methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling. …

r-foreign 0.8-80

This package provides functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files. …

r-forge 0.2.0

This package provides helper functions with a consistent interface to coerce and verify the types and shapes of values for input checking. …

r-formatr 1.7

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R…

r-formula 1.2-4

This package provides a new class `Formula', which extends the base class `formula'. It supports extended formulas with multiple parts of regressors on the right-hand side and/or multiple responses on the…

r-fourcseq 1.24.0

This package is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. `r-fourcseq' provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions.…

r-fpc 2.2-9

This package provides various methods for clustering and cluster validation. For example, it provides fixed point clustering, linear regression clustering, clustering by merging Gaussian mixture components, as well as symmetric and asymmetric…

r-fracdiff 1.5-1

This package provides tools for the maximum likelihood estimation of the parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989); it includes inference and basic methods. …

r-fractal 2.0-4

This package provides tools for stochastic fractal and deterministic chaotic time series analysis. …

r-fs 1.5.0

This package provides a cross-platform interface to file system operations, built on top of the libuv C library. …

r-furrr 0.2.1

This package provides implementations of the family of `map()' functions from the `purrr' package that can be resolved using any `future'-supported backend, e.g. parallel on the local machine or distributed on…

r-futile-logger 1.4.3

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for `cat'…

r-futile-options 1.0.1

The futile.options subsystem provides an easy user-defined options management system that is properly scoped. This means that options created via `futile.options' are fully self-contained and will not collide with options defined in…

r-future 1.20.1

The purpose of this package is to provide a lightweight and unified Future API for sequential and parallel processing of R expression via futures. This package implements sequential, multicore, multisession, and…

r-future-apply 1.6.0

This package provides implementations of `apply()', `eapply()', `lapply()', `Map()', `mapply()', `replicate()', `sapply()', `tapply()', and `vapply()' that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on…

r-gage 2.40.0

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay…

r-gagedata 2.28.0

This is a supportive data package for the software package `gage'. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general.…

r-gamlss 5.2-0

This package provides functions for fitting the generalized additive models for location scale and shape introduced by Rigby and Stasinopoulos (2005), `doi:10.1111/j.1467-9876.2005.00510.x'. The models use a distributional regression approach where all the…

r-gamlss-data 5.1-4

This package provides data used as examples to demonstrate GAMLSS models. …

r-gamlss-dist 5.1-7

This package provides a set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape. The distributions can be continuous, discrete or…

r-gamm4 0.2-6

Estimate generalized additive mixed models via a version of function `gamm' from the `mgcv' package, using the `lme4' packagefor estimation. …

r-gargle 0.5.0

This package provides utilities for working with Google APIs. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests. …

r-gaston 1.5.7

This is a package for the manipulation of genetic data (SNPs). Computation of "genetic relationship matrix" (GRM) and dominance matrix, "linkage disequilibrium" (LD), and heritability with efficient algorithms for linear mixed models…

r-gbm 2.1.8

This package is an implementation of extensions to Freund and Schapire's AdaBoost algorithm and Friedman's gradient boosting machine. It includes regression methods for least squares, absolute loss, t-distribution loss, quantile regression, logistic,…

r-gbrd 0.4-11

This package provides utilities for processing Rd objects and files. Extract argument descriptions and other parts of the help pages of functions. …

r-gclus 1.3.2

This package orders panels in scatterplot matrices and parallel coordinate displays by some merit index. It contains various indices of merit, ordering functions, and enhanced versions of `pairs' and `parcoord' which…

r-gcrma 2.62.0

Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and "non-specific binding" (NSB). The main function `gcrma' converts background adjusted probe intensities to expression measures using the same…

r-gdata 2.18.0

This package provides various R programming tools for data manipulation, including: * medical unit conversions * combining objects * character vector operations *…

r-gdina 2.8.0

This package provides a set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) `doi:10.1007/s11336-011-9207-7' and its extensions, including…

r-gdsfmt 1.26.0

This package provides a high-level R interface to CoreArray "Genomic Data Structure" (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information.…

r-gdtools 0.2.2

The `gdtools' package provides functionalities to get font metrics and to generate base64 encoded string from raster matrix. …

r-gee 4.13-20

This package provides a solver for generalized estimation equations. …

r-genalg 0.2.0

This package provides an R based genetic algorithm for binary and floating point chromosomes. …

r-genefilter 1.72.0

This package provides basic functions for filtering genes from high-throughput sequencing experiments. …

r-genelendatabase 1.18.0

This package provides the lengths of mRNA transcripts for a number of genomes and gene ID formats, largely based on the UCSC table browser. …

r-genenet 1.2.15

This package analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer…

r-geneplotter 1.68.0

This package provides functions for plotting genomic data. …

r-generics 0.1.0

In order to reduce potential package dependencies and conflicts, generics provides a number of commonly used S3 generics that are not provided by base R methods related to model fitting. …

r-genetics 1.3.8.1.2

This package provides classes and methods for handling genetic data. It includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include…

r-genie3 1.12.0

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data. …

r-genomation 1.22.0

This package provides a package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic…

r-genomationdata 1.22.0

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode. …

r-genomegraphs 1.46.0

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript…

r-genomeinfodb 1.26.2

This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural,…

r-genomeinfodbdata 1.2.0

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package. …

r-genomicalignments 1.26.0

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and…

r-genomicfeatures 1.42.1

This package provides a set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons…

r-genomicfiles 1.26.0

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation. …

r-genomicinteractions 1.24.0

This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics. …

r-genomicranges 1.42.0

This package provides tools to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The…

r-genomicscores 2.2.0

This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor. …

r-geometry 0.4.5

This package makes the qhull library available in R, in a similar manner as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace intersections about a point, Voronoi diagrams, furthest-site Delaunay triangulations,…

r-geoquery 2.58.0

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor…

r-geosphere 1.5-10

This package computes spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations. …

r-getopt 1.20.3

This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages `optparse' or `argparse' which…

r-getoptlong 1.0.4

This is yet another command-line argument parser which wraps the powerful Perl module `Getopt::Long' and with some adaptation for easier use in R. It also provides a simple way for variable…

r-getpass 0.2-2

This package provides a micro-package for reading "passwords", i.e. reading user input with masking, so that the input is not displayed as it is typed. Currently, RStudio, the command line (every…

r-ggalluvial 0.12.3

This package provides alluvial plots for `ggplot2'. Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables. …

r-ggally 2.0.0

The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data.…

r-ggbeeswarm 0.6.0

This package provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting. …

r-ggbio 1.38.0

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics…

r-ggcorrplot 0.1.3

The ggcorrplot package can be used to visualize easily a correlation matrix using ggplot2. It provides a solution for reordering the correlation matrix and displays the significance level on the plot.…

r-ggcyto 1.18.0

With the dedicated fortify method implemented for `flowSet', `ncdfFlowSet' and `GatingSet' classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The `ggcyto' wrapper and some custom…

r-ggdendro 0.1.22

This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots…

r-ggeffects 1.0.0

This package provides tools to compute marginal effects from statistical models and return the result as tidy data frames. These data frames are ready to use with the `ggplot2' package. …

r-ggextra 0.9

This package is a collection of functions and layers to enhance ggplot2. The flagship function is `ggMarginal()', which can be used to add marginal histograms/boxplots/density plots to ggplot2 scatterplots. …

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