R-universe search: needs:fastmap

rstudio

rmarkdown:Dynamic Documents for R

Convert R Markdown documents into a variety of formats.

Maintained by Yihui Xie. Last updated 2 hours ago.

literate-programming markdown pandoc rmarkdown

2.9k stars 21.80 score 14k scripts 3.7k dependents

rstudio

shiny:Web Application Framework for R

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 applications with minimal effort.

Maintained by Winston Chang. Last updated 5 days ago.

reactive rstudio shiny web-app web-development

5.5k stars 21.31 score 108k scripts 1.8k dependents

tidyverse

tidyverse:Easily Install and Load the 'Tidyverse'

The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.

Maintained by Hadley Wickham. Last updated 5 months ago.

data-science tidyverse

1.7k stars 20.23 score 664k scripts 125 dependents

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

plotly

plotly:Create Interactive Web Graphics via 'plotly.js'

Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

Maintained by Carson Sievert. Last updated 4 months ago.

d3js data-visualization ggplot2 javascript plotly shiny webgl

2.6k stars 19.43 score 93k scripts 797 dependents

haozhu233

kableExtra:Construct Complex Table with 'kable' and Pipe Syntax

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

Maintained by Hao Zhu. Last updated 25 days ago.

html kable kableextra knitr latex rmarkdown

702 stars 19.35 score 55k scripts 163 dependents

rstudio

DT:A Wrapper of the JavaScript Library 'DataTables'

Data objects in R can be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package. The package name 'DT' is an abbreviation of 'DataTables'.

Maintained by Joe Cheng. Last updated 4 months ago.

datatables htmlwidgets javascript shiny

604 stars 19.15 score 38k scripts 673 dependents

ramnathv

htmlwidgets:HTML Widgets for R

A framework for creating HTML widgets that render in various contexts including the R console, 'R Markdown' documents, and 'Shiny' web applications.

Maintained by Carson Sievert. Last updated 1 years ago.

791 stars 19.05 score 7.4k scripts 3.1k dependents

r-dbi

RSQLite:SQLite Interface for R

Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions in a recent version is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.

Maintained by Kirill Müller. Last updated 1 days ago.

database sqlite3 cpp

331 stars 18.78 score 8.1k scripts 1.1k dependents

r-lib

pkgdown:Make Static HTML Documentation for a Package

Generate an attractive and useful website from a source package. 'pkgdown' converts your documentation, vignettes, 'README', and more to 'HTML' making it easy to share information about your package online.

Maintained by Hadley Wickham. Last updated 12 days ago.

documentation-tool

734 stars 18.46 score 588 scripts 162 dependents

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 26 days ago.

docx easy-to-use html latex rtf summary-tables

2.1k stars 18.36 score 20k scripts 112 dependents

rstudio

bslib:Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'

Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.

Maintained by Carson Sievert. Last updated 26 days ago.

bootstrap htmltools rmarkdown sass shiny

511 stars 18.02 score 5.1k scripts 4.3k dependents

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 6 days ago.

fortran

209 stars 17.64 score 17k scripts 750 dependents

rstudio

htmltools:Tools for HTML

Tools for HTML generation and output.

Maintained by Carson Sievert. Last updated 11 months ago.

218 stars 17.61 score 10k scripts 4.5k dependents

rstudio

bookdown:Authoring Books and Technical Documents with R Markdown

Output formats and utilities for authoring books and technical documents with R Markdown.

Maintained by Yihui Xie. Last updated 17 days ago.

book bookdown epub gitbook html latex rmarkdown

3.9k stars 17.51 score 1.7k scripts 136 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 3 days ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

91 stars 17.40 score 7.3k scripts 303 dependents

daattali

shinyjs:Easily Improve the User Experience of Your Shiny Apps in Seconds

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 back to its original value, delaying code execution by a few seconds, and many more useful functions for both the end user and the developer. 'shinyjs' can also be used to easily call your own custom JavaScript functions from R.

Maintained by Dean Attali. Last updated 8 months ago.

javascript shiny shiny-r

740 stars 17.28 score 8.9k scripts 400 dependents

rstudio

leaflet:Create Interactive Web Maps with the JavaScript 'Leaflet' Library

Create and customize interactive maps using the 'Leaflet' JavaScript library and the 'htmlwidgets' package. These maps can be used directly from the R console, from 'RStudio', in Shiny applications and R Markdown documents.

Maintained by Joe Cheng. Last updated 27 days ago.

gis leaflet-map spatial

821 stars 17.20 score 39k scripts 178 dependents

rstudio

promises:Abstractions for Promise-Based Asynchronous Programming

Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.

Maintained by Joe Cheng. Last updated 2 months ago.

cpp

204 stars 17.10 score 688 scripts 2.6k dependents

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 8 days ago.

docx html5 ms-office-documents rmarkdown table

582 stars 17.09 score 7.3k scripts 124 dependents

dreamrs

shinyWidgets:Custom Inputs Widgets for Shiny

Collection of custom input controls and user interface components for 'Shiny' applications. Give your applications a unique and colorful style !

Maintained by Victor Perrier. Last updated 26 days ago.

shiny

849 stars 17.05 score 8.1k scripts 218 dependents

bioc

clusterProfiler:A universal enrichment tool for interpreting omics data

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Maintained by Guangchuang Yu. Last updated 4 months ago.

annotation clustering genesetenrichment go kegg multiplecomparison pathways reactome visualization enrichment-analysis gsea

1.1k stars 17.03 score 11k scripts 48 dependents

ddsjoberg

gtsummary:Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Maintained by Daniel D. Sjoberg. Last updated 6 days ago.

easy-to-use gt html5 regression-models reproducibility reproducible-research statistics summary-statistics summary-tables table1 tableone

1.1k stars 17.02 score 8.2k scripts 15 dependents

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

1.1k stars 16.96 score 9.2k scripts 111 dependents

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

2.4k stars 16.86 score 50k scripts 73 dependents

ropensci

skimr:Compact and Flexible Summaries of Data

A simple to use summary function that can be used with pipes and displays nicely in the console. The default summary statistics may be modified by the user as can the default formatting. Support for data frames and vectors is included, and users can implement their own skim methods for specific object types as described in a vignette. Default summaries include support for inline spark graphs. Instructions for managing these on specific operating systems are given in the "Using skimr" vignette and the README.

Maintained by Elin Waring. Last updated 2 months ago.

peer-reviewed ropensci summary-statistics unconf unconf17

1.1k stars 16.80 score 18k scripts 14 dependents

tidymodels

tidymodels:Easily Install and Load the 'Tidymodels' Packages

The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse.

Maintained by Max Kuhn. Last updated 1 months ago.

783 stars 16.52 score 66k scripts 15 dependents

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 3 days ago.

choropleth-maps maps spatial thematic-maps visualisation

879 stars 16.25 score 13k scripts 24 dependents

rstudio

fontawesome:Easily Work with 'Font Awesome' Icons

Easily and flexibly insert 'Font Awesome' icons into 'R Markdown' documents and 'Shiny' apps. These icons can be inserted into HTML content through inline 'SVG' tags or 'i' tags. There is also a utility function for exporting 'Font Awesome' icons as 'PNG' images for those situations where raster graphics are needed.

Maintained by Richard Iannone. Last updated 5 months ago.

font-awesome svg-icons

298 stars 16.15 score 3.1k scripts 4.3k dependents

bioc

biomaRt:Interface to BioMart databases (i.e. Ensembl)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<http://www.biomart.org>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

Maintained by Mike Smith. Last updated 17 days ago.

annotation bioconductor biomart ensembl

38 stars 15.99 score 13k scripts 230 dependents

bioc

enrichplot:Visualization of Functional Enrichment Result

The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualization methods are developed based on 'ggplot2' graphics.

Maintained by Guangchuang Yu. Last updated 3 months ago.

annotation genesetenrichment go kegg pathways software visualization enrichment-analysis pathway-analysis

239 stars 15.71 score 3.1k scripts 58 dependents

stan-dev

rstanarm:Bayesian Applied Regression Modeling via Stan

Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. Users specify models via the customary R syntax with a formula and data.frame plus some additional arguments for priors.

Maintained by Ben Goodrich. Last updated 12 days ago.

bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics multilevel-models rstan rstanarm stan statistical-modeling cpp

393 stars 15.70 score 5.0k scripts 13 dependents

r-lib

memoise:'Memoisation' of Functions

Cache the results of a function so that when you call it again with the same arguments it returns the previously computed value.

Maintained by Winston Chang. Last updated 1 years ago.

memoise

319 stars 15.67 score 824 scripts 5.3k dependents

r-lib

profvis:Interactive Visualizations for Profiling R Code

Interactive visualizations for profiling R code.

Maintained by Hadley Wickham. Last updated 6 months ago.

310 stars 15.64 score 1.3k scripts 153 dependents

facebook

prophet:Automatic Forecasting Procedure

Implements a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data. Prophet is robust to missing data and shifts in the trend, and typically handles outliers well.

Maintained by Sean Taylor. Last updated 5 months ago.

forecasting python cpp

19k stars 15.59 score 976 scripts 13 dependents

tidyverse

reprex:Prepare Reproducible Example Code via the Clipboard

Convenience wrapper that uses the 'rmarkdown' package to render small snippets of code to target formats that include both code and output. The goal is to encourage the sharing of small, reproducible, and runnable examples on code-oriented websites, such as <https://stackoverflow.com> and <https://github.com>, or in email. The user's clipboard is the default source of input code and the default target for rendered output. 'reprex' also extracts clean, runnable R code from various common formats, such as copy/paste from an R session.

Maintained by Jennifer Bryan. Last updated 7 months ago.

github reproducibility rmarkdown stackoverflow

744 stars 15.58 score 498 scripts 127 dependents

rstudio

httpuv:HTTP and WebSocket Server Library

Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)

Maintained by Winston Chang. Last updated 12 days ago.

libuv1 cpp

236 stars 15.42 score 708 scripts 2.1k dependents

rstudio

shinydashboard:Create Dashboards with 'Shiny'

Create dashboards with 'Shiny'. This package provides a theme on top of 'Shiny', making it easy to create attractive dashboards.

Maintained by Winston Chang. Last updated 3 years ago.

admin-dashboard dashboard reactivity rstudio shiny shinydashboard web-app web-development

909 stars 15.37 score 17k scripts 212 dependents

statnet

ergm:Fit, Simulate and Diagnose Exponential-Family Models for Networks

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2023) <doi:10.18637/jss.v105.i06>.

Maintained by Pavel N. Krivitsky. Last updated 21 days ago.

100 stars 15.36 score 1.4k scripts 36 dependents

bioc

GenomicFeatures:Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Maintained by H. Pagès. Last updated 5 months ago.

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

26 stars 15.34 score 5.3k scripts 339 dependents

gforge

htmlTable:Advanced Tables for Markdown/HTML

Tables with state-of-the-art layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying css-structure is simple in order to maximize compatibility with common word processors. The package also contains a few text formatting functions that help outputting text compatible with HTML/LaTeX.

Maintained by Max Gordon. Last updated 8 months ago.

knitr table

79 stars 15.33 score 1.3k scripts 767 dependents

rstudio

sass:Syntactically Awesome Style Sheets ('Sass')

An 'SCSS' compiler, powered by the 'LibSass' library. With this, R developers can use variables, inheritance, and functions to generate dynamic style sheets. The package uses the 'Sass CSS' extension language, which is stable, powerful, and CSS compatible.

Maintained by Carson Sievert. Last updated 11 months ago.

cpp

100 stars 15.30 score 252 scripts 4.3k dependents

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

1.7k stars 15.29 score 3.8k scripts 86 dependents

datastorm-open

visNetwork:Network Visualization using 'vis.js' Library

Provides an R interface to the 'vis.js' JavaScript charting library. It allows an interactive visualization of networks.

Maintained by Benoit Thieurmel. Last updated 2 years ago.

550 stars 15.25 score 4.1k scripts 196 dependents

bioc

AnnotationDbi:Manipulation of SQLite-based annotations in Bioconductor

Implements a user-friendly interface for querying SQLite-based annotation data packages.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation microarray sequencing genomeannotation bioconductor-package core-package

9 stars 15.05 score 3.6k scripts 769 dependents

quarto-dev

quarto:R Interface to 'Quarto' Markdown Publishing System

Convert R Markdown documents and 'Jupyter' notebooks to a variety of output formats using 'Quarto'.

Maintained by Christophe Dervieux. Last updated 14 days ago.

147 stars 14.98 score 1.3k scripts 36 dependents

bioc

DOSE:Disease Ontology Semantic and Enrichment analysis

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation visualization multiplecomparison genesetenrichment pathways software disease-ontology enrichment-analysis semantic-similarity

119 stars 14.97 score 2.0k scripts 61 dependents

cynkra

dm:Relational Data Models

Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.

Maintained by Kirill Müller. Last updated 3 months ago.

data-model data-warehousing datawarehousing dbi dbplyr relational-databases

511 stars 14.81 score 410 scripts 8 dependents

rstudio

learnr:Interactive Tutorials for R

Create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.

Maintained by Garrick Aden-Buie. Last updated 7 months ago.

interactive python rmarkdown shiny sql teaching tutorial

713 stars 14.79 score 6.5k scripts 27 dependents

bioc

GSVA:Gene Set Variation Analysis for Microarray and RNA-Seq Data

Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

Maintained by Robert Castelo. Last updated 10 days ago.

functionalgenomics microarray rnaseq pathways genesetenrichment gene-set-enrichment genomics pathway-enrichment-analysis

212 stars 14.74 score 1.6k scripts 19 dependents

florianhartig

DHARMa:Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models

The 'DHARMa' package uses a simulation-based approach to create readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed models. Currently supported are linear and generalized linear (mixed) models from 'lme4' (classes 'lmerMod', 'glmerMod'), 'glmmTMB', 'GLMMadaptive', and 'spaMM'; phylogenetic linear models from 'phylolm' (classes 'phylolm' and 'phyloglm'); generalized additive models ('gam' from 'mgcv'); 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model classes. Moreover, externally created simulations, e.g. posterior predictive simulations from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well. The resulting residuals are standardized to values between 0 and 1 and can be interpreted as intuitively as residuals from a linear regression. The package also provides a number of plot and test functions for typical model misspecification problems, such as over/underdispersion, zero-inflation, and residual spatial, phylogenetic and temporal autocorrelation.

Maintained by Florian Hartig. Last updated 27 days ago.

glmm regression regression-diagnostics residual

226 stars 14.74 score 2.8k scripts 10 dependents

husson

FactoMineR:Multivariate Exploratory Data Analysis and Data Mining

Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).

Maintained by Francois Husson. Last updated 4 months ago.

47 stars 14.71 score 5.6k scripts 112 dependents

rstudio

crosstalk:Inter-Widget Interactivity for HTML Widgets

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

Maintained by Carson Sievert. Last updated 3 months ago.

292 stars 14.69 score 1.6k scripts 1.5k dependents

dcomtois

summarytools:Tools to Quickly and Neatly Summarize Data

Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.

Maintained by Dominic Comtois. Last updated 5 days ago.

descriptive-statistics frequency-table html-report markdown pander pandoc pandoc-markdown rmarkdown rstudio

527 stars 14.62 score 2.9k scripts 6 dependents

glin

reactable:Interactive Data Tables for R

Interactive data tables for R, based on the 'React Table' JavaScript library. Provides an HTML widget that can be used in 'R Markdown' or 'Quarto' documents, 'Shiny' applications, or viewed from an R console.

Maintained by Greg Lin. Last updated 2 months ago.

htmlwidgets react shiny table

648 stars 14.57 score 3.3k scripts 158 dependents

bioc

TCGAbiolinks:TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

Maintained by Tiago Chedraoui Silva. Last updated 1 months ago.

dnamethylation differentialmethylation generegulation geneexpression methylationarray differentialexpression pathways network sequencing survival software bioc bioconductor gdc integrative-analysis tcga tcga-data tcgabiolinks

310 stars 14.47 score 1.6k scripts 6 dependents

rstudio

plumber:An API Generator for R

Gives the ability to automatically generate and serve an HTTP API from R functions using the annotations in the R documentation around your functions.

Maintained by Barret Schloerke. Last updated 20 days ago.

api api-server plumber

1.4k stars 14.47 score 2.2k scripts 16 dependents

r-lidar

lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.

Maintained by Jean-Romain Roussel. Last updated 2 months ago.

als forestry las laz lidar point-cloud remote-sensing openblas cpp openmp

623 stars 14.47 score 844 scripts 8 dependents

indrajeetpatil

ggstatsplot:'ggplot2' Based Plots with Statistical Details

Extension of 'ggplot2', 'ggstatsplot' creates graphics with details from statistical tests included in the plots themselves. It provides an easier syntax to generate information-rich plots for statistical analysis of continuous (violin plots, scatterplots, histograms, dot plots, dot-and-whisker plots) or categorical (pie and bar charts) data. Currently, it supports the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian versions of t-test/ANOVA, correlation analyses, contingency table analysis, meta-analysis, and regression analyses. References: Patil (2021) <doi:10.21105/joss.03236>.

Maintained by Indrajeet Patil. Last updated 1 months ago.

bayes-factors datascience dataviz effect-size ggplot-extension hypothesis-testing non-parametric-statistics regression-models statistical-analysis

2.1k stars 14.46 score 3.0k scripts 1 dependents

r-spatial

mapview:Interactive Viewing of Spatial Data in R

Quickly and conveniently create interactive visualisations of spatial data with or without background maps. Attributes of displayed features are fully queryable via pop-up windows. Additional functionality includes methods to visualise true- and false-color raster images and bounding boxes.

Maintained by Tim Appelhans. Last updated 3 months ago.

gis leaflet maps spatial visualization web-mapping

526 stars 14.39 score 7.3k scripts 27 dependents

davidgohel

ggiraph:Make 'ggplot2' Graphics Interactive

Create interactive 'ggplot2' graphics using 'htmlwidgets'.

Maintained by David Gohel. Last updated 3 days ago.

libpng cpp

822 stars 14.37 score 4.1k scripts 35 dependents

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 17 days ago.

immunooncology massspectrometry metabolomics bioconductor feature-detection mass-spectrometry peak-detection cpp

196 stars 14.31 score 984 scripts 11 dependents

talgalili

heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.

Maintained by Tal Galili. Last updated 9 months ago.

d3-heatmap dendextend dendrogram ggplot2 heatmap plotly

386 stars 14.21 score 2.0k scripts 45 dependents

thinkr-open

golem:A Framework for Robust Shiny Applications

An opinionated framework for building a production-ready 'Shiny' application. This package contains a series of tools for building a robust 'Shiny' application from start to finish.

Maintained by Colin Fay. Last updated 7 months ago.

golemverse hacktoberfest shiny shiny-apps shiny-r shinyapps

921 stars 14.21 score 167 scripts 63 dependents

business-science

timetk:A Tool Kit for Working with Time Series

Easy visualization, wrangling, and feature engineering of time series data for forecasting and machine learning prediction. Consolidates and extends time series functionality from packages including 'dplyr', 'stats', 'xts', 'forecast', 'slider', 'padr', 'recipes', and 'rsample'.

Maintained by Matt Dancho. Last updated 1 years ago.

coercion coercion-functions data-mining dplyr forecast forecasting forecasting-models machine-learning series-decomposition series-signature tibble tidy tidyquant tidyverse time time-series timeseries

626 stars 14.20 score 4.0k scripts 16 dependents

kassambara

factoextra:Extract and Visualize the Results of Multivariate Data Analyses

Provides some easy-to-use functions to extract and visualize the output of multivariate data analyses, including 'PCA' (Principal Component Analysis), 'CA' (Correspondence Analysis), 'MCA' (Multiple Correspondence Analysis), 'FAMD' (Factor Analysis of Mixed Data), 'MFA' (Multiple Factor Analysis) and 'HMFA' (Hierarchical Multiple Factor Analysis) functions from different R packages. It contains also functions for simplifying some clustering analysis steps and provides 'ggplot2' - based elegant data visualization.

Maintained by Alboukadel Kassambara. Last updated 5 years ago.

363 stars 14.13 score 15k scripts 52 dependents

bioc

GOSemSim:GO-terms Semantic Similarity Measures

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation go clustering pathways network software bioinformatics gene-ontology semantic-similarity cpp

63 stars 14.12 score 708 scripts 68 dependents

r-lib

conflicted:An Alternative Conflict Resolution Strategy

R's default conflict management system gives the most recently loaded package precedence. This can make it hard to detect conflicts, particularly when they arise because a package update creates ambiguity that did not previously exist. 'conflicted' takes a different approach, making every conflict an error and forcing you to choose which function to use.

Maintained by Hadley Wickham. Last updated 1 years ago.

conflicts

250 stars 14.09 score 6.0k scripts 147 dependents

react-r

reactR:React Helpers

Make it easy to use 'React' in R with 'htmlwidget' scaffolds, helper dependency functions, an embedded 'Babel' 'transpiler', and examples.

Maintained by Kent Russell. Last updated 7 months ago.

html htmlwidgets javascript react reactjs web

414 stars 14.09 score 109 scripts 175 dependents

bioc

ensembldb:Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Maintained by Johannes Rainer. Last updated 5 months ago.

genetics annotationdata sequencing coverage annotation bioconductor bioconductor-packages ensembl

35 stars 14.08 score 892 scripts 108 dependents

rstudio

chromote:Headless Chrome Web Browser Interface

An implementation of the 'Chrome DevTools Protocol', for controlling a headless Chrome web browser.

Maintained by Garrick Aden-Buie. Last updated 5 days ago.

164 stars 13.96 score 162 scripts 28 dependents

hughjonesd

huxtable:Easily Create and Style Tables for LaTeX, HTML and Other Formats

Creates styled tables for data presentation. Export to HTML, LaTeX, RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate borders, size, position, captions, colours, text styles and number formatting. Table cells can span multiple rows and/or columns. Includes a 'huxreg' function for creation of regression tables, and 'quick_*' one-liners to print data to a new document.

Maintained by David Hugh-Jones. Last updated 27 days ago.

html huxtable latex microsoft-word powerpoint reproducible-research tables

323 stars 13.93 score 1.9k scripts 16 dependents

jbkunst

highcharter:A Wrapper for the 'Highcharts' Library

A wrapper for the 'Highcharts' library including shortcut functions to plot R objects. 'Highcharts' <https://www.highcharts.com/> is a charting library offering numerous chart types with a simple configuration syntax.

Maintained by Joshua Kunst. Last updated 1 years ago.

highcharts htmlwidgets shiny shiny-r visualization wrapper

725 stars 13.93 score 4.9k scripts 18 dependents

hrbrmstr

hrbrthemes:Additional Themes, Theme Components and Utilities for 'ggplot2'

A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' is also included.

Maintained by Bob Rudis. Last updated 17 days ago.

data-visualization datavisualization ggplot-extension ggplot2 ggplot2-scales ggplot2-themes visualization

1.3k stars 13.92 score 13k scripts 15 dependents

daattali

shinycssloaders:Add Loading Animations to a 'shiny' Output While It's Recalculating

When a 'Shiny' output (such as a plot, table, map, etc.) is recalculating, it remains visible but gets greyed out. Using 'shinycssloaders', you can add a loading animation ("spinner") to outputs instead. By wrapping a 'Shiny' output in 'withSpinner()', a spinner will automatically appear while the output is recalculating. You can also manually show and hide the spinner, or add a full-page spinner to cover the entire page. See the demo online at <https://daattali.com/shiny/shinycssloaders-demo/>.

Maintained by Dean Attali. Last updated 13 days ago.

shiny shiny-r

410 stars 13.92 score 4.3k scripts 120 dependents

bioc

AnnotationHub:Client to access AnnotationHub resources

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure dataimport gui thirdpartyclient core-package u24ca289073

17 stars 13.88 score 2.7k scripts 104 dependents

rinterface

shinydashboardPlus:Add More 'AdminLTE2' Components to 'shinydashboard'

Extend 'shinydashboard' with 'AdminLTE2' components. 'AdminLTE2' is a free 'Bootstrap 3' dashboard template available at <https://adminlte.io>. Customize boxes, add timelines and a lot more.

Maintained by David Granjon. Last updated 8 months ago.

dashboard hacktoberfest2022 shiny shiny-apps shinydashboard

461 stars 13.82 score 1.1k scripts 28 dependents

r-spatial

rgee:R Bindings for Calling the 'Earth Engine' API

Earth Engine <https://earthengine.google.com/> client library for R. All of the 'Earth Engine' API classes, modules, and functions are made available. Additional functions implemented include importing (exporting) of Earth Engine spatial objects, extraction of time series, interactive map display, assets management interface, and metadata display. See <https://r-spatial.github.io/rgee/> for further details.

Maintained by Cesar Aybar. Last updated 4 days ago.

earth-engine earthengine google-earth-engine googleearthengine spatial-analysis spatial-data

717 stars 13.77 score 1.9k scripts 3 dependents

bioc

BiocFileCache:Manage Files Across Sessions

This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

Maintained by Lori Shepherd. Last updated 2 months ago.

dataimport core-package u24ca289073

13 stars 13.76 score 486 scripts 436 dependents

bioc

mixOmics:Omics Data Integration Project

Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Maintained by Eva Hamrud. Last updated 3 days ago.

immunooncology microarray sequencing metabolomics metagenomics proteomics geneprediction multiplecomparison classification regression bioconductor genomics genomics-data genomics-visualization multivariate-analysis multivariate-statistics omics r-pkg r-project

185 stars 13.75 score 1.3k scripts 22 dependents

r-lib

cachem:Cache R Objects with Automatic Pruning

Key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.

Maintained by Winston Chang. Last updated 11 months ago.

59 stars 13.67 score 68 scripts 5.4k dependents

insightsengineering

rtables:Reporting Tables

Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.

Maintained by Joe Zhu. Last updated 3 months ago.

pharmaceuticals tables

232 stars 13.65 score 238 scripts 17 dependents

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 27 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

274 stars 13.63 score 1.6k scripts 23 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 11 days ago.

845 stars 13.63 score 264 scripts 2 dependents

christophergandrud

networkD3:D3 JavaScript Network Graphs from R

Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.

Maintained by Christopher Gandrud. Last updated 6 years ago.

d3js networks

654 stars 13.60 score 3.4k scripts 31 dependents

rstudio

dygraphs:Interface to 'Dygraphs' Interactive Time Series Charting Library

An R interface to the 'dygraphs' JavaScript charting library (a copy of which is included in the package). Provides rich facilities for charting time-series data in R, including highly configurable series- and axis-display and interactive features like zoom/pan and series/point highlighting.

Maintained by Petr Shevtsov. Last updated 2 years ago.

365 stars 13.48 score 3.6k scripts 65 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 days ago.

visualization graphandnetwork thirdpartyclient network

52 stars 13.47 score 628 scripts 17 dependents

daattali

ggExtra:Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements

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.

Maintained by Dean Attali. Last updated 10 months ago.

ggplot2 ggplot2-enhancements marginal-plots

387 stars 13.45 score 3.3k scripts 28 dependents

vincentarelbundock

modelsummary:Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready

Create beautiful and customizable tables to summarize several statistical models side-by-side. Draw coefficient plots, multi-level cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and correlation matrices. This package supports dozens of statistical models, and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr' dynamic documents. Details can be found in Arel-Bundock (2022) <doi:10.18637/jss.v103.i01>.

Maintained by Vincent Arel-Bundock. Last updated 30 days ago.

927 stars 13.39 score 6.2k scripts 2 dependents

business-science

tidyquant:Tidy Quantitative Financial Analysis

Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant' package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR' and 'PerformanceAnalytics' package functions and returns the objects in the tidy 'tibble' format. The main advantage is being able to use quantitative functions with the 'tidyverse' functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See the 'tidyquant' website for more information, documentation and examples.

Maintained by Matt Dancho. Last updated 2 months ago.

dplyr financial-analysis financial-data financial-statements multiple-stocks performance-analysis performanceanalytics quantmod stock stock-exchanges stock-indexes stock-lists stock-performance stock-prices stock-symbol tidyverse time-series timeseries xts

872 stars 13.34 score 5.2k scripts

dreamrs

esquisse:Explore and Visualize Your Data Interactively

A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics. You can quickly visualize your data accordingly to their type, export in various formats, and retrieve the code to reproduce the plot.

Maintained by Victor Perrier. Last updated 1 months ago.

addin data-visualization ggplot2 rstudio-addin visualization

1.8k stars 13.31 score 1.1k scripts 1 dependents

trafficonese

leaflet.extras:Extra Functionality for 'leaflet' Package

The 'leaflet' JavaScript library provides many plugins some of which are available in the core 'leaflet' package, but there are many more. It is not possible to support them all in the core 'leaflet' package. This package serves as an add-on to the 'leaflet' package by providing extra functionality via 'leaflet' plugins.

Maintained by Sebastian Gatscha. Last updated 3 months ago.

data-visualization geospatial leaflet

218 stars 13.27 score 2.5k scripts 25 dependents

rstudio

shinythemes:Themes for Shiny

Themes for use with Shiny. Includes several Bootstrap themes from <https://bootswatch.com/>, which are packaged for use with Shiny applications.

Maintained by Winston Chang. Last updated 3 years ago.

155 stars 13.20 score 8.5k scripts 125 dependents

wadpac

GGIR:Raw Accelerometer Data Analysis

A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.

Maintained by Vincent T van Hees. Last updated 17 days ago.

accelerometer activity-recognition circadian-rhythm movement-sensor sleep

109 stars 13.20 score 342 scripts 3 dependents

stan-dev

shinystan:Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models

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 'Shiny' web application framework from 'RStudio' and works with the output of MCMC programs written in any programming language (and has extended functionality for 'Stan' models fit using the 'rstan' and 'rstanarm' packages).

Maintained by Jonah Gabry. Last updated 3 years ago.

bayesian bayesian-data-analysis bayesian-inference bayesian-methods bayesian-statistics mcmc shiny-apps stan statistical-graphics

200 stars 13.13 score 1.6k scripts 15 dependents

lchiffon

wordcloud2:Create Word Cloud by htmlWidget

A fast visualization tool for creating wordcloud by using wordcloud2.js.

Maintained by Dawei Lang. Last updated 7 years ago.

402 stars 13.10 score 2.8k scripts 11 dependents

tagteam

riskRegression:Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

Implementation of the following methods for event history analysis. Risk regression models for survival endpoints also in the presence of competing risks are fitted using binomial regression based on a time sequence of binary event status variables. A formula interface for the Fine-Gray regression model and an interface for the combination of cause-specific Cox regression models. A toolbox for assessing and comparing performance of risk predictions (risk markers and risk prediction models). Prediction performance is measured by the Brier score and the area under the ROC curve for binary possibly time-dependent outcome. Inverse probability of censoring weighting and pseudo values are used to deal with right censored data. Lists of risk markers and lists of risk models are assessed simultaneously. Cross-validation repeatedly splits the data, trains the risk prediction models on one part of each split and then summarizes and compares the performance across splits.

Maintained by Thomas Alexander Gerds. Last updated 1 months ago.

openblas cpp

47 stars 13.07 score 736 scripts 37 dependents

keaven

gsDesign:Group Sequential Design

Derives group sequential clinical trial designs and describes their properties. Particular focus on time-to-event, binary, and continuous outcomes. Largely based on methods described in Jennison, Christopher and Turnbull, Bruce W., 2000, "Group Sequential Methods with Applications to Clinical Trials" ISBN: 0-8493-0316-8.

Maintained by Keaven Anderson. Last updated 27 days ago.

biostatistics boundaries clinical-trials design spending-functions

51 stars 13.05 score 338 scripts 5 dependents

bioc

Gviz:Plotting data and annotation information along genomic coordinates

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

Maintained by Robert Ivanek. Last updated 5 months ago.

visualization microarray sequencing

79 stars 13.05 score 1.4k scripts 46 dependents

bioc

ChIPseeker:ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Maintained by Guangchuang Yu. Last updated 5 months ago.

annotation chipseq software visualization multiplecomparison atac-seq chip-seq comparison epigenetics epigenomics

233 stars 13.05 score 1.6k scripts 5 dependents

ggrothendieck

sqldf:Manipulate R Data Frames Using SQL

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, imports the data frames into that database, performs the SQL select or other statement and returns the result using a heuristic to determine which class to assign to each column of the returned data frame. The sqldf() or read.csv.sql() functions can also be used to read filtered files into R even if the original files are larger than R itself can handle. 'RSQLite', 'RH2', 'RMySQL' and 'RPostgreSQL' backends are supported.

Maintained by G. Grothendieck. Last updated 3 years ago.

250 stars 13.04 score 8.1k scripts 52 dependents

appsilon

shiny.semantic:Semantic UI Support for Shiny

Creating a great user interface for your Shiny apps can be a hassle, especially if you want to work purely in R and don't want to use, for instance HTML templates. This package adds support for a powerful UI library Fomantic UI - <https://fomantic-ui.com/> (before Semantic). It also supports universal UI input binding that works with various DOM elements.

Maintained by Jakub Nowicki. Last updated 12 months ago.

appsilon fomantic-ui rhinoverse semantic semantic-components semantic-ui shiny

506 stars 13.00 score 586 scripts 3 dependents

ropensci

piggyback:Managing Larger Data on a GitHub Repository

Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.

Maintained by Carl Boettiger. Last updated 4 months ago.

data-store git-lfs peer-reviewed

187 stars 12.98 score 187 scripts 12 dependents

tidyverse

ellmer:Chat with Large Language Models

Chat with large language models from a range of providers including 'Claude' <https://claude.ai>, 'OpenAI' <https://chatgpt.com>, and more. Supports streaming, asynchronous calls, tool calling, and structured data extraction.

Maintained by Hadley Wickham. Last updated 3 days ago.

407 stars 12.94 score 98 scripts 8 dependents

juba

questionr:Functions to Make Surveys Processing Easier

Set of functions to make the processing and analysis of surveys easier : interactive shiny apps and addins for data recoding, contingency tables, dataset metadata handling, and several convenience functions.

Maintained by Julien Barnier. Last updated 10 days ago.

83 stars 12.93 score 1.1k scripts 19 dependents

yixuan

prettydoc:Creating Pretty Documents from R Markdown

Creating tiny yet beautiful documents and vignettes from R Markdown. The package provides the 'html_pretty' output format as an alternative to the 'html_document' and 'html_vignette' engines that convert R Markdown into HTML pages. Various themes and syntax highlight styles are supported.

Maintained by Yixuan Qiu. Last updated 4 years ago.

html markdown r-markdown

486 stars 12.90 score 550 scripts 8 dependents

friendly

matlib:Matrix Functions for Teaching and Learning Linear Algebra and Multivariate Statistics

A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods. Many of these functions are designed for tutorial purposes in learning matrix algebra ideas using R. In some cases, functions are provided for concepts available elsewhere in R, but where the function call or name is not obvious. In other cases, functions are provided to show or demonstrate an algorithm. In addition, a collection of functions are provided for drawing vector diagrams in 2D and 3D and for rendering matrix expressions and equations in LaTeX.

Maintained by Michael Friendly. Last updated 16 days ago.

diagrams linear-equations matrix matrix-functions matrix-visualizer vector vignette

65 stars 12.89 score 900 scripts 11 dependents

johncoene

waiter:Loading Screen for 'Shiny'

Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.

Maintained by John Coene. Last updated 12 months ago.

hacktoberfest shiny

496 stars 12.87 score 702 scripts 68 dependents

rinterface

bs4Dash:A 'Bootstrap 4' Version of 'shinydashboard'

Make 'Bootstrap 4' Shiny dashboards. Use the full power of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4' <https://github.com/ColorlibHQ/AdminLTE>.

Maintained by David Granjon. Last updated 7 months ago.

bootstrap4 dashboard-templates hacktoberfest2022 shiny shiny-apps shinydashboard

442 stars 12.87 score 1.2k scripts 15 dependents

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 25 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

225 stars 12.86 score 380 scripts 9 dependents

markedmondson1234

googleAuthR:Authenticate and Create Google APIs

Create R functions that interact with OAuth2 Google APIs <https://developers.google.com/apis-explorer/> easily, with auto-refresh and Shiny compatibility.

Maintained by Erik Grönroos. Last updated 10 months ago.

api authentication google googleauthr oauth2-flow shiny

178 stars 12.85 score 804 scripts 13 dependents

bioc

minfi:Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Maintained by Kasper Daniel Hansen. Last updated 4 months ago.

immunooncology dnamethylation differentialmethylation epigenetics microarray methylationarray multichannel twochannel dataimport normalization preprocessing qualitycontrol

60 stars 12.82 score 996 scripts 27 dependents

davidgohel

gdtools:Utilities for Graphical Rendering and Fonts Management

Tools are provided to compute metrics of formatted strings and to check the availability of a font. Another set of functions is provided to support the collection of fonts from 'Google Fonts' in a cache. Their use is simple within 'R Markdown' documents and 'shiny' applications but also with graphic productions generated with the 'ggiraph', 'ragg' and 'svglite' packages or with tabular productions from the 'flextable' package.

Maintained by David Gohel. Last updated 6 days ago.

cairo freetype cpp

26 stars 12.80 score 234 scripts 152 dependents

bioc

EBImage:Image processing and analysis toolbox for R

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

Maintained by Andrzej Oleś. Last updated 5 months ago.

visualization bioinformatics image-analysis image-processing cpp

71 stars 12.77 score 1.5k scripts 33 dependents

bioc

MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Maintained by Laurent Gatto. Last updated 17 days ago.

immunooncology infrastructure proteomics massspectrometry qualitycontrol dataimport bioconductor bioinformatics mass-spectrometry proteomics-data visualisation cpp

131 stars 12.76 score 772 scripts 36 dependents

r-lib

downlit:Syntax Highlighting and Automatic Linking

Syntax highlighting of R code, specifically designed for the needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and 'bookdown'. It includes linking of function calls to their documentation on the web, and automatic translation of ANSI escapes in output to the equivalent HTML.

Maintained by Hadley Wickham. Last updated 10 months ago.

syntax-highlighting

90 stars 12.72 score 364 scripts 176 dependents

yihui

xaringan:Presentation Ninja

Create HTML5 slides with R Markdown and the JavaScript library 'remark.js' (<https://remarkjs.com>).

Maintained by Yihui Xie. Last updated 1 years ago.

markdown naruto ninja presentation presentation-ninja remarkjs rmarkdown rstudio slideshow

1.5k stars 12.69 score 948 scripts 10 dependents

insightsengineering

teal:Exploratory Web Apps for Analyzing Clinical Trials Data

A 'shiny' based interactive exploration framework for analyzing clinical trials data. 'teal' currently provides a dynamic filtering facility and different data viewers. 'teal' 'shiny' applications are built using standard 'shiny' modules.

Maintained by Dawid Kaledkowski. Last updated 1 months ago.

clinical-trials nest shiny webapp

206 stars 12.65 score 176 scripts 5 dependents

bioc

SpatialExperiment:S4 Class for Spatially Resolved -omics Data

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

Maintained by Dario Righelli. Last updated 5 months ago.

datarepresentation dataimport infrastructure immunooncology geneexpression transcriptomics singlecell spatial

59 stars 12.63 score 1.8k scripts 71 dependents

thibautjombart

adegenet:Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Maintained by Zhian N. Kamvar. Last updated 2 months ago.

182 stars 12.60 score 1.9k scripts 29 dependents

hrbrmstr

ggalt:Extra Coordinate Systems, 'Geoms', Statistical Transformations, Scales and Fonts for 'ggplot2'

A compendium of new geometries, coordinate systems, statistical transformations, scales and fonts for 'ggplot2', including splines, 1d and 2d densities, univariate average shifted histograms, a new map coordinate system based on the 'PROJ.4'-library along with geom_cartogram() that mimics the original functionality of geom_map(), formatters for "bytes", a stat_stepribbon() function, increased 'plotly' compatibility and the 'StateFace' open source font 'ProPublica'. Further new functionality includes lollipop charts, dumbbell charts, the ability to encircle points and coordinate-system-based text annotations.

Maintained by Bob Rudis. Last updated 2 years ago.

geom ggplot-extension ggplot2 ggplot2-geom ggplot2-scales

676 stars 12.60 score 2.3k scripts 7 dependents

massimoaria

bibliometrix:Comprehensive Science Mapping Analysis

Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.

Maintained by Massimo Aria. Last updated 12 days ago.

bibliometric-analysis bibliometrics citation citation-network citations co-authors co-occurence co-word-analysis correspondence-analysis coupling isi-web journal manuscript quantitative-analysis scholars science science-mapping scientific scientometrics scopus

545 stars 12.54 score 518 scripts 2 dependents

yihui

servr:A Simple HTTP Server to Serve Static Files or Dynamic Documents

Start 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.

Maintained by Yihui Xie. Last updated 3 months ago.

http-server web-server websocket

283 stars 12.51 score 190 scripts 94 dependents

insightsengineering

tern:Create Common TLGs Used in Clinical Trials

Table, Listings, and Graphs (TLG) library for common outputs used in clinical trials.

Maintained by Joe Zhu. Last updated 2 months ago.

clinical-trials graphs listings nest outputs tables

83 stars 12.50 score 186 scripts 9 dependents

rstudio

flexdashboard:R Markdown Format for Flexible Dashboards

Format for converting an R Markdown document to a grid oriented dashboard. The dashboard flexibly adapts the size of it's components to the containing web page.

Maintained by Garrick Aden-Buie. Last updated 11 months ago.

823 stars 12.49 score 4.5k scripts 8 dependents

r-spatial

leafem:'leaflet' Extensions for 'mapview'

Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.

Maintained by Tim Appelhans. Last updated 1 months ago.

108 stars 12.41 score 704 scripts 55 dependents

trevorld

ggpattern:'ggplot2' Pattern Geoms

Provides 'ggplot2' geoms filled with various patterns. Includes a patterned version of every 'ggplot2' geom that has a region that can be filled with a pattern. Provides a suite of 'ggplot2' aesthetics and scales for controlling pattern appearances. Supports over a dozen builtin patterns (every pattern implemented by 'gridpattern') as well as allowing custom user-defined patterns.

Maintained by Trevor L. Davis. Last updated 2 months ago.

370 stars 12.36 score 1.7k scripts 3 dependents

bioc

TFBSTools:Software Package for Transcription Factor Binding Site (TFBS) Analysis

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Maintained by Ge Tan. Last updated 19 days ago.

motifannotation generegulation motifdiscovery transcription alignment

28 stars 12.36 score 1.1k scripts 18 dependents

irkernel

repr:Serializable Representations

String and binary representations of objects for several formats / mime types.

Maintained by Philipp Angerer. Last updated 8 months ago.

53 stars 12.35 score 2.2k scripts 45 dependents

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

262 stars 12.35 score 406 scripts 14 dependents

jrowen

rhandsontable:Interface to the 'Handsontable.js' Library

An R interface to the 'Handsontable' JavaScript library, which is a minimalist Excel-like data grid editor. See <https://handsontable.com/> for details.

Maintained by Jonathan Owen. Last updated 3 years ago.

handsontable htmlwidgets javascript shiny sparkline

389 stars 12.31 score 1.0k scripts 46 dependents

eliocamp

metR:Tools for Easier Analysis of Meteorological Fields

Many useful functions and extensions for dealing with meteorological data in the tidy data framework. Extends 'ggplot2' for better plotting of scalar and vector fields and provides commonly used analysis methods in the atmospheric sciences.

Maintained by Elio Campitelli. Last updated 11 days ago.

atmospheric-science ggplot2 visualization

146 stars 12.30 score 1000 scripts 22 dependents

nflverse

nflreadr:Download 'nflverse' Data

A minimal package for downloading data from 'GitHub' repositories of the 'nflverse' project.

Maintained by Tan Ho. Last updated 4 months ago.

nfl nflfastr nflverse sports-data

67 stars 12.29 score 476 scripts 10 dependents

bioc

ReactomePA:Reactome Pathway Analysis

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. This package is not affiliated with the Reactome team.

Maintained by Guangchuang Yu. Last updated 5 months ago.

pathways visualization annotation multiplecomparison genesetenrichment reactome enrichment-analysis reactome-pathway-analysis reactomepa

40 stars 12.25 score 1.5k scripts 7 dependents

bioc

ggbio:Visualization tools for genomic data

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 data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

Maintained by Michael Lawrence. Last updated 5 months ago.

infrastructure visualization

111 stars 12.23 score 734 scripts 16 dependents

rsquaredacademy

olsrr:Tools for Building OLS Regression Models

Tools designed to make it easier for users, particularly beginner/intermediate R users to build ordinary least squares regression models. Includes comprehensive regression output, heteroskedasticity tests, collinearity diagnostics, residual diagnostics, measures of influence, model fit assessment and variable selection procedures.

Maintained by Aravind Hebbali. Last updated 5 months ago.

collinearity-diagnostics linear-models regression stepwise-regression

103 stars 12.19 score 1.4k scripts 4 dependents

ebailey78

shinyBS:Extra Twitter Bootstrap Components for Shiny

Adds easy access to additional Twitter Bootstrap components to Shiny.

Maintained by Eric Bailey. Last updated 9 years ago.

183 stars 12.19 score 3.1k scripts 101 dependents

rstudio

shinytest2:Testing for Shiny Applications

Automated unit testing of Shiny applications through a headless 'Chromium' browser.

Maintained by Barret Schloerke. Last updated 5 days ago.

cpp

108 stars 12.13 score 704 scripts 1 dependents

geomorphr

geomorph:Geometric Morphometric Analyses of 2D and 3D Landmark Data

Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.

Maintained by Dean Adams. Last updated 2 months ago.

76 stars 12.05 score 700 scripts 6 dependents

dreamrs

fresh:Create Custom 'Bootstrap' Themes to Use in 'Shiny'

Customize 'Bootstrap' and 'Bootswatch' themes, like colors, fonts, grid layout, to use in 'Shiny' applications, 'rmarkdown' documents and 'flexdashboard'.

Maintained by Victor Perrier. Last updated 9 months ago.

bootstrap shiny shiny-applications shiny-themes

228 stars 12.03 score 546 scripts 47 dependents

dreamrs

datamods:Modules to Import and Manipulate Data in 'Shiny'

'Shiny' modules to import data into an application or 'addin' from various sources, and to manipulate them after that.

Maintained by Victor Perrier. Last updated 26 days ago.

shiny shiny-modules

144 stars 12.03 score 174 scripts 7 dependents

crsh

papaja:Prepare American Psychological Association Journal Articles with R Markdown

Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.

Maintained by Frederik Aust. Last updated 1 months ago.

apa apa-guidelines journal manuscript psychology reproducible-paper reproducible-research rmarkdown

663 stars 12.00 score 1.7k scripts 2 dependents

bioc

ExperimentHub:Client to access ExperimentHub resources

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure dataimport gui thirdpartyclient core-package u24ca289073

10 stars 11.94 score 764 scripts 57 dependents

jinghuazhao

gap:Genetic Analysis Package

As first reported [Zhao, J. H. 2007. "gap: Genetic Analysis Package". J Stat Soft 23(8):1-18. <doi:10.18637/jss.v023.i08>], it is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, probability of familial disease aggregation, kinship calculation, statistics in linkage analysis, and association analysis involving genetic markers including haplotype analysis with or without environmental covariates. Over years, the package has been developed in-between many projects hence also in line with the name (gap).

Maintained by Jing Hua Zhao. Last updated 6 days ago.

genetics imputation lmm fortran

12 stars 11.94 score 448 scripts 16 dependents

rstudio

rticles:Article Formats for R Markdown

A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.

Maintained by Christophe Dervieux. Last updated 20 days ago.

article journal paper rmarkdown

1.5k stars 11.93 score 188 scripts 3 dependents

rstudio

r2d3:Interface to 'D3' Visualizations

Suite of tools for using 'D3', a library for producing dynamic, interactive data visualizations. Supports translating objects into 'D3' friendly data structures, rendering 'D3' scripts, publishing 'D3' visualizations, incorporating 'D3' in R Markdown, creating interactive 'D3' applications with Shiny, and distributing 'D3' based 'htmlwidgets' in R packages.

Maintained by Nick Strayer. Last updated 3 years ago.

d3 r2d3 visualization

519 stars 11.88 score 498 scripts 10 dependents

bioc

QFeatures:Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Maintained by Laurent Gatto. Last updated 27 days ago.

infrastructure massspectrometry proteomics metabolomics bioconductor mass-spectrometry

27 stars 11.87 score 278 scripts 49 dependents

trestletech

shinyAce:Ace Editor Bindings for Shiny

Ace editor bindings to enable a rich text editing environment within Shiny.

Maintained by Vincent Nijs. Last updated 2 months ago.

222 stars 11.86 score 388 scripts 64 dependents

rinterface

shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities

Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).

Maintained by David Granjon. Last updated 2 months ago.

android hacktoberfest2022 pwa shiny shinyapps template

410 stars 11.85 score 1.1k scripts 2 dependents

irkernel

IRkernel:Native R Kernel for the 'Jupyter Notebook'

The R kernel for the 'Jupyter' environment executes R code which the front-end ('Jupyter Notebook' or other front-ends) submits to the kernel via the network.

Maintained by Philipp Angerer. Last updated 11 months ago.

jupyter jupyter-kernels jupyter-notebook zmq

1.7k stars 11.78 score 139 scripts 23 dependents

r-causal

ggdag:Analyze and Create Elegant Directed Acyclic Graphs

Tidy, analyze, and plot directed acyclic graphs (DAGs). 'ggdag' is built on top of 'dagitty', an R package that uses the 'DAGitty' web tool (<https://dagitty.net/>) for creating and analyzing DAGs. 'ggdag' makes it easy to tidy and plot 'dagitty' objects using 'ggplot2' and 'ggraph', as well as common analytic and graphical functions, such as determining adjustment sets and node relationships.

Maintained by Malcolm Barrett. Last updated 8 months ago.

causal-inference dag ggplot-extension

443 stars 11.78 score 1.8k scripts 5 dependents

friendly

heplots:Visualizing Hypothesis Tests in Multivariate Linear Models

Provides HE plot and other functions for visualizing hypothesis tests in multivariate linear models. HE plots represent sums-of-squares-and-products matrices for linear hypotheses and for error using ellipses (in two dimensions) and ellipsoids (in three dimensions). The related 'candisc' package provides visualizations in a reduced-rank canonical discriminant space when there are more than a few response variables.

Maintained by Michael Friendly. Last updated 8 days ago.

linear-hypotheses matrices multivariate-linear-models plot repeated-measure-designs visualizing-hypothesis-tests

9 stars 11.78 score 1.1k scripts 7 dependents

thomasp85

shinyFiles:A Server-Side File System Viewer for Shiny

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 file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.

Maintained by Thomas Lin Pedersen. Last updated 2 years ago.

filemanager shiny ui-components

199 stars 11.77 score 736 scripts 62 dependents

daattali

colourpicker:A Colour Picker Tool for Shiny and for Selecting Colours in Plots

A colour picker that can be used as an input in 'Shiny' apps or Rmarkdown documents. The colour picker supports alpha opacity, custom colour palettes, and many more options. A Plot Colour Helper tool is available as an 'RStudio' Addin, which helps you pick colours to use in your plots. A more generic Colour Picker 'RStudio' Addin is also provided to let you select colours to use in your R code.

Maintained by Dean Attali. Last updated 8 months ago.

rstudio-addin shiny shiny-r

222 stars 11.76 score 936 scripts 120 dependents

datalorax

equatiomatic:Transform Models into 'LaTeX' Equations

The goal of 'equatiomatic' is to reduce the pain associated with writing 'LaTeX' formulas from fitted models. The primary function of the package, extract_eq(), takes a fitted model object as its input and returns the corresponding 'LaTeX' code for the model.

Maintained by Philippe Grosjean. Last updated 22 days ago.

619 stars 11.75 score 424 scripts 5 dependents

rstudio

pagedown:Paginate the HTML Output of R Markdown with CSS for Print

Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.

Maintained by Yihui Xie. Last updated 3 months ago.

css html paged-media pdf printing typesetting

909 stars 11.73 score 350 scripts 19 dependents

jbryer

likert:Analysis and Visualization Likert Items

An approach to analyzing Likert response items, with an emphasis on visualizations. The stacked bar plot is the preferred method for presenting Likert results. Tabular results are also implemented along with density plots to assist researchers in determining whether Likert responses can be used quantitatively instead of qualitatively. See the likert(), summary.likert(), and plot.likert() functions to get started.

Maintained by Jason Bryer. Last updated 5 days ago.

data-science visualization

310 stars 11.71 score 480 scripts 2 dependents

bwlewis

threejs:Interactive 3D Scatter Plots, Networks and Globes

Create interactive 3D scatter plots, network plots, and globes using the 'three.js' visualization library (<https://threejs.org>).

Maintained by B. W. Lewis. Last updated 3 years ago.

data-visualization graph-animation igraph threejs webgl

304 stars 11.67 score 522 scripts 28 dependents

jthomasmock

gtExtras:Extending 'gt' for Beautiful HTML Tables

Provides additional functions for creating beautiful tables with 'gt'. The functions are generally wrappers around boilerplate or adding opinionated niche capabilities and helpers functions.

Maintained by Thomas Mock. Last updated 12 months ago.

data-science data-visualization datascience ggplot2 gt plots sparkline sparkline-graphs sparklines tables

201 stars 11.66 score 2.4k scripts 5 dependents

mrkaye97

slackr:Send Messages, Images, R Objects and Files to 'Slack' Channels/Users

'Slack' <https://slack.com/> provides a service for teams to collaborate by sharing messages, images, links, files and more. Functions are provided that make it possible to interact with the 'Slack' platform 'API'. When you need to share information or data from R, rather than resort to copy/ paste in e-mails or other services like 'Skype' <https://www.skype.com/en/>, you can use this package to send well-formatted output from multiple R objects and expressions to all teammates at the same time with little effort. You can also send images from the current graphics device, R objects, and upload files.

Maintained by Matt Kaye. Last updated 6 months ago.

slack

306 stars 11.66 score 179 scripts

haleyjeppson

ggmosaic:Mosaic Plots in the 'ggplot2' Framework

Mosaic plots in the 'ggplot2' framework. Mosaic plot functionality is provided in a single 'ggplot2' layer by calling the geom 'mosaic'.

Maintained by Haley Jeppson. Last updated 6 months ago.

167 stars 11.63 score 1.8k scripts 4 dependents

pecanproject

PEcAn.data.atmosphere:PEcAn Functions Used for Managing Climate Driver Data

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.

Maintained by David LeBauer. Last updated 7 hours ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

216 stars 11.63 score 64 scripts 14 dependents

rstudio

sortable:Drag-and-Drop in 'shiny' Apps with 'SortableJS'

Enables drag-and-drop behaviour in Shiny apps, by exposing the functionality of the 'SortableJS' <https://sortablejs.github.io/Sortable/> JavaScript library as an 'htmlwidget'. You can use this in Shiny apps and widgets, 'learnr' tutorials as well as R Markdown. In addition, provides a custom 'learnr' question type - 'question_rank()' - that allows ranking questions with drag-and-drop.

Maintained by Andrie de Vries. Last updated 7 months ago.

htmlwidget

135 stars 11.62 score 368 scripts 13 dependents

bioc

bumphunter:Bump Hunter

Tools for finding bumps in genomic data

Maintained by Tamilselvi Guharaj. Last updated 5 months ago.

dnamethylation epigenetics infrastructure multiplecomparison immunooncology

16 stars 11.61 score 210 scripts 43 dependents

rstudio

blogdown:Create Blogs and Websites with R Markdown

Write blog posts and web pages in R Markdown. This package supports the static site generator 'Hugo' (<https://gohugo.io>) best, and it also supports 'Jekyll' (<https://jekyllrb.com>) and 'Hexo' (<https://hexo.io>).

Maintained by Yihui Xie. Last updated 15 days ago.

blog-engine blogdown hugo rmarkdown rstudio website-generation

1.8k stars 11.55 score 1.4k scripts 1 dependents

tylermorganwall

rayshader:Create Maps and Visualize Data in 2D and 3D

Uses a combination of raytracing and multiple hill shading methods to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hill shading, 2D and 3D plotting options, a built-in path tracer, 'Wavefront' OBJ file export, and the ability to save 3D visualizations to a 3D printable format.

Maintained by Tyler Morgan-Wall. Last updated 2 months ago.

cpp

2.1k stars 11.55 score 1.5k scripts 5 dependents

functionaldata

fdapace:Functional Data Analysis and Empirical Dynamics

A versatile package that provides implementation of various methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this package is Functional Principal Component Analysis (FPCA), a key technique for functional data analysis, for sparsely or densely sampled random trajectories and time courses, via the Principal Analysis by Conditional Estimation (PACE) algorithm. This core algorithm yields covariance and mean functions, eigenfunctions and principal component (scores), for both functional data and derivatives, for both dense (functional) and sparse (longitudinal) sampling designs. For sparse designs, it provides fitted continuous trajectories with confidence bands, even for subjects with very few longitudinal observations. PACE is a viable and flexible alternative to random effects modeling of longitudinal data. There is also a Matlab version (PACE) that contains some methods not available on fdapace and vice versa. Updates to fdapace were supported by grants from NIH Echo and NSF DMS-1712864 and DMS-2014626. Please cite our package if you use it (You may run the command citation("fdapace") to get the citation format and bibtex entry). References: Wang, J.L., Chiou, J., Müller, H.G. (2016) <doi:10.1146/annurev-statistics-041715-033624>; Chen, K., Zhang, X., Petersen, A., Müller, H.G. (2017) <doi:10.1007/s12561-015-9137-5>.

Maintained by Yidong Zhou. Last updated 9 months ago.

cpp

31 stars 11.54 score 474 scripts 25 dependents

workflowr

workflowr:A Framework for Reproducible and Collaborative Data Science

Provides a workflow for your analysis projects by combining literate programming ('knitr' and 'rmarkdown') and version control ('Git', via 'git2r') to generate a website containing time-stamped, versioned, and documented results.

Maintained by John Blischak. Last updated 4 months ago.

git project-management rmarkdown website workflow

848 stars 11.53 score 566 scripts

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 3 days ago.

distance openstreetmap router shortest-paths street-networks cpp

129 stars 11.52 score 229 scripts 4 dependents

bioc

systemPipeR:systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Maintained by Thomas Girke. Last updated 5 months ago.

genetics infrastructure dataimport sequencing rnaseq riboseq chipseq methylseq snp geneexpression coverage genesetenrichment alignment qualitycontrol immunooncology reportwriting workflowstep workflowmanagement

53 stars 11.52 score 344 scripts 3 dependents

johncoene

echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5

Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.

Maintained by David Munoz Tord. Last updated 17 days ago.

echarts hacktoberfest htmlwidget htmlwidgets visualization

603 stars 11.45 score 1.3k scripts 11 dependents

sachaepskamp

qgraph:Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation

Fork of qgraph - Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.

Maintained by Sacha Epskamp. Last updated 1 years ago.

cpp

69 stars 11.43 score 1.2k scripts 63 dependents

epimodel

EpiModel:Mathematical Modeling of Infectious Disease Dynamics

Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims. Full methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Maintained by Samuel Jenness. Last updated 2 months ago.

agent-based-modeling epidemics epidemiology infectious-diseases network-graph cpp

250 stars 11.43 score 315 scripts

bioc

annotate:Annotation for microarrays

Using R enviroments for annotation.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

annotation pathways go

11.41 score 812 scripts 239 dependents

lazappi

clustree:Visualise Clusterings at Different Resolutions

Deciding what resolution to use can be a difficult question when approaching a clustering analysis. One way to approach this problem is to look at how samples move as the number of clusters increases. This package allows you to produce clustering trees, a visualisation for interrogating clusterings as resolution increases.

Maintained by Luke Zappia. Last updated 1 years ago.

clustering clustering-trees visualisation visualization

219 stars 11.40 score 1.9k scripts 5 dependents

bioc

VariantAnnotation:Annotation of Genetic Variants

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Maintained by Bioconductor Package Maintainer. Last updated 3 months ago.

dataimport sequencing snp annotation genetics variantannotation curl bzip2 xz-utils zlib

11.39 score 1.9k scripts 152 dependents

openintrostat

openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs

Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.

Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.

data openintro

240 stars 11.39 score 6.0k scripts

bioc

PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data

Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.

Maintained by Benjamin Haibe-Kains. Last updated 3 months ago.

geneexpression pharmacogenetics pharmacogenomics software classification datasets pharmacogenomic pharmacogx cpp

68 stars 11.39 score 442 scripts 3 dependents

r4ss

r4ss:R Code for Stock Synthesis

A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.23.1, from December 2024). Support for 3.24 models is only through the core functions for reading output and plotting.

Maintained by Ian G. Taylor. Last updated 20 days ago.

fisheries fisheries-stock-assessment stock-synthesis

43 stars 11.38 score 1.0k scripts 2 dependents

doi-usgs

nhdplusTools:NHDPlus Tools

Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.

Maintained by David Blodgett. Last updated 1 months ago.

87 stars 11.38 score 348 scripts 5 dependents

bioc

pathview:a tool set for pathway based data integration and visualization

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

Maintained by Weijun Luo. Last updated 2 days ago.

pathways graphandnetwork visualization genesetenrichment differentialexpression geneexpression microarray rnaseq genetics metabolomics proteomics systemsbiology sequencing

40 stars 11.37 score 1.6k scripts 10 dependents

rolkra

explore:Simplifies Exploratory Data Analysis

Interactive data exploration with one line of code, automated reporting or use an easy to remember set of tidy functions for low code exploratory data analysis.

Maintained by Roland Krasser. Last updated 18 hours ago.

data-exploration data-visualisation decision-trees eda rmarkdown shiny tidy

230 stars 11.36 score 221 scripts 1 dependents

ropensci

biomartr:Genomic Data Retrieval

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.

Maintained by Hajk-Georg Drost. Last updated 2 months ago.

biomart genomic-data-retrieval annotation-retrieval database-retrieval ncbi ensembl biological-data-retrieval ensembl-servers genome genome-annotation genome-retrieval genomics meta-analysis metagenomics ncbi-genbank peer-reviewed proteome sequenced-genomes

218 stars 11.35 score 129 scripts 3 dependents

dsy109

mixtools:Tools for Analyzing Finite Mixture Models

Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).

Maintained by Derek Young. Last updated 10 months ago.

mixture-models mixture-of-experts semiparametric-regression

20 stars 11.34 score 1.4k scripts 56 dependents

bioc

BiocStyle:Standard styles for vignettes and other Bioconductor documents

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

software bioconductor-package core-package

12 stars 11.31 score 1.2k scripts 47 dependents

neuhausi

canvasXpress:Visualization Package for CanvasXpress in R

Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.

Maintained by Connie Brett. Last updated 3 days ago.

analytics bioinformatics chart charting dash dashboard data-analytics data-science data-visualization genomics graphs javascript network network-visualization python reproducible-research shiny visualization

297 stars 11.28 score 145 scripts

mrcieu

TwoSampleMR:Two Sample MR Functions and Interface to MRC Integrative Epidemiology Unit OpenGWAS Database

A package for performing Mendelian randomization using GWAS summary data. It uses the IEU OpenGWAS database <https://gwas.mrcieu.ac.uk/> to automatically obtain data, and a wide range of methods to run the analysis.

Maintained by Gibran Hemani. Last updated 3 days ago.

476 stars 11.27 score 1.7k scripts 1 dependents

bioc

karyoploteR:Plot customizable linear genomes displaying arbitrary data

karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.

Maintained by Bernat Gel. Last updated 5 months ago.

visualization copynumbervariation sequencing coverage dnaseq chipseq methylseq dataimport onechannel bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r

307 stars 11.25 score 656 scripts 4 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

Maintained by Matthew L. Fidler. Last updated 2 months ago.

fortran openblas cpp openmp

40 stars 11.24 score 220 scripts 13 dependents

dreamrs

shinybusy:Busy Indicators and Notifications for 'Shiny' Applications

Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy. And other tools to let your users know something is happening (send notifications, reports, ...).

Maintained by Victor Perrier. Last updated 7 months ago.

shiny

144 stars 11.23 score 772 scripts 39 dependents

rstudio

leaflet.providers:Leaflet Providers

Contains third-party map tile provider information from 'Leaflet.js', <https://github.com/leaflet-extras/leaflet-providers>, to be used with the 'leaflet' R package. Additionally, 'leaflet.providers' enables users to retrieve up-to-date provider information between package updates.

Maintained by Barret Schloerke. Last updated 1 years ago.

14 stars 11.22 score 408 scripts 180 dependents

tidyverse

duckplyr:A 'DuckDB'-Backed Version of 'dplyr'

A drop-in replacement for 'dplyr', powered by 'DuckDB' for performance. Offers convenient utilities for working with in-memory and larger-than-memory data while retaining full 'dplyr' compatibility.

Maintained by Kirill Müller. Last updated 4 days ago.

analytics dataframe dplyr duckdb performance

313 stars 11.22 score 220 scripts

boxuancui

DataExplorer:Automate Data Exploration and Treatment

Automated data exploration process for analytic tasks and predictive modeling, so that users could focus on understanding data and extracting insights. The package scans and analyzes each variable, and visualizes them with typical graphical techniques. Common data processing methods are also available to treat and format data.

Maintained by Boxuan Cui. Last updated 1 years ago.

data-analysis data-exploration data-science eda visualization

523 stars 11.21 score 2.2k scripts

rstudio

webshot2:Take Screenshots of Web Pages

Takes screenshots of web pages, including Shiny applications and R Markdown documents. 'webshot2' uses headless Chrome or Chromium as the browser back-end.

Maintained by Winston Chang. Last updated 2 months ago.

114 stars 11.20 score 928 scripts 17 dependents

ropensci

EML:Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Maintained by Carl Boettiger. Last updated 3 years ago.

eml eml-metadata metadata-standard

97 stars 11.19 score 378 scripts 7 dependents

benjaminrich

table1:Tables of Descriptive Statistics in HTML

Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.

Maintained by Benjamin Rich. Last updated 2 years ago.

81 stars 11.17 score 1.5k scripts 6 dependents

daattali

shinyalert:Easily Create Pretty Popup Messages (Modals) in 'Shiny'

Easily create pretty popup messages (modals) in 'Shiny'. A modal can contain text, images, OK/Cancel buttons, an input to get a response from the user, and many more customizable options.

Maintained by Dean Attali. Last updated 10 months ago.

shiny shiny-r

243 stars 11.16 score 1.3k scripts 25 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 11 days ago.

fortran openblas

36 stars 11.16 score 398 scripts 2 dependents

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 3 days ago.

49 stars 11.16 score 332 scripts 2 dependents

wlandau

crew:A Distributed Worker Launcher Framework

In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.

Maintained by William Michael Landau. Last updated 3 days ago.

high-performance-computing

136 stars 11.13 score 243 scripts 2 dependents