Packages — R (Page 16 of 51)

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### r-scran 1.20.1

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly…

### r-scrime 1.3.5

This package provides tools for the analysis of high-dimensional data developed/implemented at the group "Statistical Complexity Reduction In Molecular Epidemiology" (SCRIME). The main focus is on SNP data, but most of the…

### r-scrypt 0.1.3

This package provides functions for working with the scrypt key derivation functions. Scrypt is a password-based key derivation function created by Colin Percival. The algorithm was specifically designed to make…

### r-sctransform 0.3.2

This package provides a normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As…

### r-scuttle 1.2.1

This package provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. It also provides some helper functions to assist development of other packages. …

### r-sdmtools 1.1-221.2

This package provides a set of tools for post processing the outcomes of species distribution modeling exercises. It includes novel methods for comparing models and tracking changes in distributions through time.…

### r-seewave 2.1.8

This package provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and…

### r-segmented 1.3-4

Given a regression model, segmented updates the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed. …

### r-selectr 0.4-2

`r-selectr' translates a CSS3 selector into an equivalent XPath expression. This allows you to use CSS selectors when working with the XML package as it can only evaluate XPath expressions. …

### r-sem 3.1-11

This package provides functions for fitting general linear structural equation models (with observed and latent variables) using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares. …

### r-semplot 1.1.2

Structural equation modeling (SEM) has a long history of representing models graphically as path diagrams. The semPlot package for R fills the gap between advanced, but time-consuming, graphical software and the…

### r-semtools 0.5-5

This package provides useful tools for structural equation modeling. …

### r-semver 0.2.0

This package provides tools and functions for parsing, rendering and operating on semantic version strings. Semantic versioning is a simple set of rules and requirements that dictate how version numbers are…

### r-sendmailr 1.2-1

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R. …

### r-seqbias 1.40.0

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads…

### r-seqgl 1.1.4

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between…

### r-seqinr 4.2-8

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system. …

### r-seqlogo 1.58.0

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990). …

### r-seqminer 8.0

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R. …

### r-seqpattern 1.24.0

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature. …

### r-seriation 1.3.0

This package provides infrastructure for seriation with an implementation of several seriation/sequencing techniques to reorder matrices, dissimilarity matrices, and dendrograms. It also provides (optimally) reordered heatmaps, color images and clustering visualizations like…

### r-servr 0.23

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory. …

### r-sessioninfo 1.1.1

This package provides tools to query and print information about the current R session. It is similar to `utils::sessionInfo()', but includes more information about packages, and where they were installed from. …

### r-sets 1.0-18

This package provides data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals. …

### r-seurat 4.0.4

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality…

### r-seuratdisk 0.0.0.9019-1.163f1aa

The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information…

### r-seuratobject 4.0.2

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure…

### r-sf 1.0-2

This package provides support for simple features, a standardized way to encode spatial vector data. It binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to…

### r-sfsmisc 1.1-12

This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics. …

### r-sgloptim 1.3.8

This package provides a fast generic solver for sparse group lasso optimization problems. The loss (objective) function must be defined in a C++ module. The optimization problem is solved using…

### r-sgseq 1.26.0

SGSeq is a package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice…

### r-shades 1.4.0

This package provides functions for easily manipulating colors, creating color scales and calculating color distances. …

### r-shadowtext 0.0.9

This package implements `shadowtextGrob()' for `grid' and `geom_shadowtext()' layer for `ggplot2'. These functions draw text grob with background shadow. …

### r-shaman 2.0-2.d6944e8

The Shaman package implements functions for resampling Hi-C matrices in order to generate expected contact distributions given constraints on marginal coverage and contact-distance probability distributions. The package also provides support for visualizing…

### r-shape 1.4.6

This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ... …

### r-shapes 1.2.6

This package provides routines for the statistical analysis of landmark shapes, including Procrustes analysis, graphical displays, principal components analysis, permutation and bootstrap tests, thin-plate spline transformation grids and comparing covariance matrices. See…

### r-shapforxgboost 0.1.1

The aim of `SHAPforxgboost' is to aid in visual data investigations using "SHAP" (Shapley additive explanation) visualization plots for `XGBoost'. It provides summary plot, dependence plot, interaction plot, and force plot.…

### r-shiny 1.6.0

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful…

### r-shinyace 0.4.1

This package provides Ace editor bindings to enable a rich text editing environment within Shiny. …

### r-shinybs 0.61

This package adds additional Twitter Bootstrap components to Shiny. …

### r-shinycell 2.0.0-1.aecbd56

This package provides Shiny apps for interactive exploration of single-cell data. …

### r-shinycssloaders 1.0.0

This package provides tools to create a lightweight Shiny wrapper for the css-loaders created by Luke Hass `https://github.com/lukehaas/css-loaders'. Wrapping a Shiny output will automatically show a loader when the output is (re)calculating. …

### r-shinydashboard 0.7.1

This package provides an extension to the Shiny web application framework for R, making it easy to create attractive dashboards. …

### r-shinyfiles 0.9.0

This package provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the…

### r-shinyjqui 0.4.0

This is an extension to Shiny that brings interactions and animation effects from the jQuery UI library. …

### r-shinyjs 2.0.0

Perform common useful JavaScript operations in Shiny apps that will greatly improve your apps without having to know any JavaScript. Examples include: hiding an element, disabling an input, resetting an input…

### r-shinystan 2.5.0

This package provides a graphical user interface for interactive "Markov chain Monte Carlo" (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by the…

### r-shinythemes 1.2.0

This package provides themes for use with Shiny. It includes several Bootstrap themes, which are packaged for use with Shiny applications. …

### r-shinytree 0.2.7

This package exposes R bindings to jsTree, a JavaScript library that supports interactive trees, to enable rich, editable trees in Shiny. …

### r-shortread 1.50.0

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 0.9-4

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 1.66.0

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-signac 1.1.1-1.e0512d3

This package provides a framework for the analysis and exploration of single-cell chromatin data. The Signac package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and…

### r-signal 0.7-7

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 1.60.0

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-simplifyenrichment 1.2.0

This package provides a new clustering algorithm, binary cut, for clustering similarity matrices of functional terms is implemented in this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings. …

### r-singlecellexperiment 1.14.1

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 1.1.8

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 2.8.7

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 2.8.9

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 0.18.1

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 0.2.2

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-slingshot 2.0.0

This package provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an…

### 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 2.2-5.7

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 2.0.0

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 1.42.0

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-sodium 1.1

This package provides bindings to libsodium: a library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a Diffie-Hellman function by Daniel Bernstein, which has become very popular after it…

### r-softimpute 1.4-1

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 2.28.0

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 1.4-5

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 2.7-0

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 1.81

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 1.4.2

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 7.3-14

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 2.2-0

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-core 2.3-0

This is a subset of the original spatstat package, containing all of the user-level code from spatstat, except for the code for linear networks. …