Packages — R (Page 14 of 39)

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r-shortread 1.48.0

This package implements sampling, iteration, and input of FASTQ files. It includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as `DNAStringSet'-derived objects,…

r-showtext 0.9-1

This package aims to make it easy to use various types of fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports most output formats of R graphics including…

r-showtextdb 3.0

This package provides font files that can be used by the `showtext' package. …

r-siggenes 1.64.0

This package provides tools for the identification of differentially expressed genes and estimation of the "False Discovery Rate" (FDR) using both the Significance Analysis of Microarrays (SAM) and the "Empirical Bayes Analyses…

r-signal 0.7-6

This package provides a set of signal processing functions originally written for Matlab and GNU Octave. It includes filter generation utilities, filtering functions, resampling routines, and visualization of filter models. …

r-sigpathway 1.58.0

This package is used to conduct pathway analysis by calculating the NT_k and NE_k statistics in a statistical framework for determining whether a specified group of genes for a pathway has a…

r-simpleaffy 2.66.0

This package provides high level functions for reading Affy `.CEL' files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy…

r-singlecellexperiment 1.12.0

This package defines an S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along…

r-sitmo 2.0.1

This package provides two high quality and fast PPRNGs that may be used in an OpenMP parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence. …

r-sjlabelled 1.1.7

This package provides a collection of functions dealing with labelled data, like reading and writing data between R and other statistical software packages. This includes easy ways to get, set or…

r-sjmisc 2.8.5

This package is a collection of miscellaneous utility functions, supporting data transformation tasks like recoding, dichotomizing or grouping variables, setting and replacing missing values. The data transformation functions also support labelled data,…

r-sjplot 2.8.6

This package represents a collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this…

r-sjstats 0.18.0

This package provides a collection of convenient functions for common statistical computations, which are not directly provided by R's `base' or `stats' packages. This package aims at providing, first, shortcuts for statistical…

r-slam 0.1-48

This package contains data structures and algorithms for sparse arrays and matrices, based on index arrays and simple triplet representations, respectively. …

r-slider 0.1.5

This package provides type-stable rolling window functions over any R data type. Cumulative and expanding windows are also supported. For more advanced usage, an index can be used as a secondary…

r-sloop 1.0.1

This package provides a collection of helper functions designed to help you to better understand object oriented programming in R, particularly using `S3'. …

r-sm 2.2-5.6

This is software accompanying the book 'Applied Smoothing Techniques for Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford University Press. It provides smoothing methods for nonparametric regression and density estimation …

r-smoother 1.1

This package provides a collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of…

r-smpracticals 1.4-3

This package contains the datasets and a few functions for use with the practicals outlined in Appendix A of the book Statistical Models (Davison, 2003, Cambridge University Press). The practicals themselves…

r-sn 1.6-2

This package provides functionalities to build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provides related statistical methods for data fitting and diagnostics, in…

r-sna 2.6

This package provides a range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization. …

r-snakecase 0.11.0

This package provides a consistent, flexible and easy to use tool to parse and convert strings into cases like snake or camel among others. …

r-snapatac 2.0

This package provides a fast and accurate analysis toolkit for single cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing). Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and…

r-snow 0.4-3

The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls `makeCluster' to start a cluster of worker processes; the master…

r-snowballc 0.7.0

This package provides an R interface to the C `libstemmer' library that implements Porter's word stemming algorithm for collapsing words to a common root to aid comparison of vocabulary. Currently supported…

r-snowfall 1.84-6.1

This package is a usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in…

r-snp-plotter 0.5.1

This package helps you create plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a "linkage disequilibrium" (LD) plot and the ability…

r-snplocs-hsapiens-dbsnp144-grch37 0.99.20

This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30,…

r-snpmaxsel 1.0-3

This package implements asymptotic methods related to maximally selected statistics, with applications to "single-nucleotide polymorphism" (SNP) data. …

r-snpstats 1.40.0

This package provides classes and statistical methods for large "single-nucleotide polymorphism" (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes. …

r-softimpute 1.4

This package provides iterative methods for matrix completion that use nuclear-norm regularization. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank "single value decompositions" (SVDs)…

r-somaticsignatures 2.26.0

This package identifies mutational signatures of "single nucleotide variants" (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms. …

r-soupx 0.3.1-1.a3354be

This package provides a package for quantifying, profiling and removing cell free mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. …

r-sourcetools 0.1.7

The sourcetools package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code. …

r-sp 1.4-4

This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting…

r-spacyr 1.2.1

This package provides an R wrapper to the Python "natural language processing" (NLP) library `spaCy', from `http://spacy.io'. …

r-spam 2.5-1

This package provides a set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: 1. it only supports (essentially) one sparse matrix format; 2.…

r-spams 2.6-2017-03-22

SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the following problems: 1. Dictionary learning and matrix factorization (NMF, sparse…

r-sparql 1.16

This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point. …

r-sparselda 0.1-9

This package performs sparse linear discriminant analysis for Gaussians and mixture of Gaussian models. …

r-sparsem 1.78

This package provides some basic linear algebra functionality for sparse matrices. It includes Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products. …

r-sparsematrixstats 1.2.0

This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format. …

r-sparsesvd 0.2

This package provides a Wrapper around the SVDLIBC library for (truncated) singular value decomposition of a sparse matrix. Currently, only sparse real matrices in Matrix package format are supported. …

r-spatial 7.3-12

This package provides functions for kriging and point pattern analysis. …

r-spatialextremes 2.0-9

This package provides tools for the statistical modelling of spatial extremes using max-stable processes, copula or Bayesian hierarchical models. More precisely, this package allows (conditional) simulations from various parametric max-stable models, analysis…

r-spatstat 1.64-1

This package provides a comprehensive toolbox for analysing Spatial Point Patterns. It is focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. It also supports three-dimensional point…

r-spatstat-data 1.5-2

This package contains all the datasets for the `spatstat' package. …

r-spatstat-utils 1.17-0

This package contains utility functions for the `spatstat' package which may also be useful for other purposes. …

r-spdata 0.3.8

This a package containing diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis. It includes R data of class `sf', `Spatial', and `nb'. It also contains data stored…

r-spdep 1.1-5

This package provides a collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use…

r-spectrum 1.1

This package provides a self-tuning spectral clustering method for single or multi-view data. Spectrum uses a new type of adaptive density aware kernel that strengthens connections in the graph based on…

r-speedglm 0.3-2

This package provides tools for fitting linear models and generalized linear models to large data sets by updating algorithms. …

r-splitstackshape 1.4.8

Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The `concat.split' (cSplit) family of functions provided by this package splits such data into separate…

r-splus2r 1.2-2

Currently there are many functions in S-PLUS that are missing in R. To facilitate the conversion of S-PLUS packages to R packages, this package provides some missing S-PLUS functionality in R. …

r-sqldf 0.4-11

The `sqldf' function is typically passed a single argument which is an SQL select statement where the table names are ordinary R data frame names. `sqldf' transparently sets up a database,…

r-squarem 2020.5

This package provides algorithms for accelerating the convergence of slow, monotone sequences from smooth, contraction mapping such as the EM algorithm. It can be used to accelerate any smooth, linearly convergent…

r-stabledist 0.7-1

This package provides density, probability and quantile functions, and random number generation for (skew) stable distributions, using the parametrizations of Nolan. …

r-stabs 0.6-3

This package provides resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection…

r-stam 0.0-1

This package provides various methods to conduct Spatio-Temporal Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and Inferred Spatio-Temporal Modelling. …

r-stanheaders 2.21.0-6

The C++ header files of the Stan project are provided by this package. There is a shared object containing part of the `CVODES' library, but it is not accessible from R.…

r-statcheck 1.3.0

This package can automatically extract statistical null-hypothesis significant testing (NHST) results from articles and recompute the p-values based on the reported test statistic and degrees of freedom to detect possible inconsistencies. …

r-statmod 1.4.35

This package provides a collection of algorithms and functions to aid statistical modeling. It includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss…

r-statnet-common 4.4.1

This package provides non-statistical utilities used by the software developed by the Statnet Project. …

r-stepwise 0.3

This package provides a stepwise approach to identifying recombination breakpoints in a genomic sequence alignment. …

r-stm 1.3.6

The "Structural Topic Model" (STM) allows researchers to estimate topic models with document-level covariates. The package also includes tools for model selection, visualization, and estimation of topic-covariate regressions. …

r-stopwords 2.1

This package provides multiple sources of stopwords, for use in text analysis and natural language processing. …

r-stringdist 0.9.6.3

This package implements an approximate string matching version of R's native `match' function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine,…

r-stringi 1.5.3

This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the…

r-stringr 1.4.0

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic `stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s…

r-strucchange 1.5-2

This package provides tools for testing, monitoring and dating structural changes in (linear) regression models. It features tests/methods from the generalized fluctuation test framework as well as from the F test…

r-styler 1.3.2

This is a package for pretty-printing R code without changing the user's formatting intent. …

r-subplex 1.6

This package implements the Subplex optimization algorithm. It solves unconstrained optimization problems using a simplex method on subspaces. The method is well suited for optimizing objective functions that are noisy…

r-summarizedexperiment 1.20.0

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent…

r-summarytools 0.9.6

This package provides tools for data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good…

r-suppdists 1.1-9.5

This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores…

r-survey 4.0

This package provides tools for the analysis of complex survey samples. The provided features include: summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and…

r-survival 3.2-7

This package contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models. …

r-survivalroc 1.0.3

Compute time-dependent ROC curve from censored survival data using Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty, Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344) …

r-survminer 0.4.8

This package contains the function `ggsurvplot()' for easily drawing beautiful and 'ready-to-publish' survival curves with the 'number at risk' table and 'censoring count plot'. Other functions are also available to plot…

r-survmisc 0.5.5

This package provides a collection of functions to help in the analysis of right-censored survival data. These extend the methods available in the `survival' package. …

r-sushi 1.28.0

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures. …

r-sva 3.38.0

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are…

r-svdialogs 1.0.0

This package helps to construct standard dialog boxes for your GUI, including message boxes, input boxes, list, file or directory selection, and others. In case R cannot display GUI dialog boxes,…

r-svglite 1.2.3.2

`svglite' is a graphics device that produces clean "SVG" (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in `svg()', `svglite' is considerably faster,…

r-svgui 1.0.0

The SciViews `svGUI' package eases the management of Graphical User Interfaces (GUI) in R. It is independent from any particular GUI widgets. It centralizes info about GUI elements currently used,…

r-svmisc 1.1.0

This package provides miscellaneous functions for SciViews or general use, including tools to manage a temporary environment attached to the search path for temporary variables you do not want to `save()' or…

r-synchronicity 1.3.5

This package provides support for synchronization via mutexes and may eventually support interprocess communication and message passing. …

r-sys 3.4

This package provides drop-in replacements for the base `system2()' function with fine control and consistent behavior across platforms. It supports clean interruption, timeout, background tasks, and streaming STDIN / STDOUT /…

r-sysfonts 0.8.2

This is a package to simplify loading of system fonts and Google Fonts into R, in order to support other packages. …

r-systemfonts 0.3.2

This package provides system native access to the font catalogue. As font handling varies between systems it is difficult to correctly locate installed fonts across different operating systems. The 'systemfonts'…

r-systempiper 1.24.2

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of "next generation sequence" (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features…

r-tab 4.1.1

This package contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional…

r-tam 3.5-19

This package includes tools for marginal maximum likelihood estimation and joint maximum likelihood estimation for unidimensional and multidimensional item response models. The package functionality covers the Rasch model, 2PL model, 3PL model,…

r-tcltk2 1.2-11

This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package …

r-tclust 1.4-2

This package implements different robust clustering algorithms (`tclust') based on trimming and including some graphical diagnostic tools (`ctlcurves' and `DiscrFact'). …

r-tdthap 1.1-11

Functions and examples are provided for transmission/disequilibrium tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999) "Transmission/disequilibrium tests for extended marker haplotypes". …

r-tea 1.1

This package provides different approaches for selecting the threshold in generalized Pareto distributions. Most of them are based on minimizing the AMSE-criterion or at least by reducing the bias of the…

r-tensor 1.5

The tensor product of two arrays is notionally an outer product of the arrays collapsed in specific extents by summing along the appropriate diagonals. This package allows you to compute the…

r-tensora 0.36.2

This package provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate…

r-testthat 3.0.0

This package provides a unit testing system for R designed to be fun, flexible and easy to set up. …

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