R-universe search: needs:fs

rstudio

rmarkdown:Dynamic Documents for R

Convert R Markdown documents into a variety of formats.

Maintained by Yihui Xie. Last updated 3 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 6 days ago.

reactive rstudio shiny web-app web-development

5.5k stars 21.31 score 108k scripts 1.8k dependents

r-lib

testthat:Unit Testing for R

Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.

Maintained by Hadley Wickham. Last updated 1 months ago.

unit-testing cpp

900 stars 20.99 score 74k scripts 471 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-lib

roxygen2:In-Line Documentation for R

Generate your Rd documentation, 'NAMESPACE' file, and collation field using specially formatted comments. Writing documentation in-line with code makes it easier to keep your documentation up-to-date as your requirements change. 'roxygen2' is inspired by the 'Doxygen' system for C++.

Maintained by Hadley Wickham. Last updated 8 months ago.

devtools documentation cpp

606 stars 18.51 score 2.3k scripts 219 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

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 26 days ago.

github setup

869 stars 17.54 score 5.6k scripts 336 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 28 days ago.

gis leaflet-map spatial

821 stars 17.20 score 39k scripts 178 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

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

bioc

ggtree:an R package for visualization of tree and annotation data

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Maintained by Guangchuang Yu. Last updated 5 months ago.

alignment annotation clustering dataimport multiplesequencealignment phylogenetics reproducibleresearch software visualization annotations ggplot2 phylogenetic-trees

871 stars 16.83 score 5.1k scripts 109 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 3 days ago.

fortran cpp

86 stars 16.73 score 7.7k scripts 101 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

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

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

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

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

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

tidyverse

googledrive:An Interface to Google Drive

Manage Google Drive files from R.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive

329 stars 14.97 score 2.1k scripts 164 dependents

philchalmers

mirt:Multidimensional Item Response Theory

Analysis of discrete response data using unidimensional and multidimensional item analysis models under the Item Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>). Exploratory and confirmatory item factor analysis models are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier models are available for modeling item testlets using dimension reduction EM algorithms, while multiple group analyses and mixed effects designs are included for detecting differential item, bundle, and test functioning, and for modeling item and person covariates. Finally, latent class models such as the DINA, DINO, multidimensional latent class, mixture IRT models, and zero-inflated response models are supported, as well as a wide family of probabilistic unfolding models.

Maintained by Phil Chalmers. Last updated 4 days ago.

irt mirt openblas cpp openmp

212 stars 14.93 score 2.5k scripts 40 dependents

r-lib

gargle:Utilities for Working with Google APIs

Provides utilities for working with Google APIs <https://developers.google.com/apis-explorer>. This includes functions and classes for handling common credential types and for preparing, executing, and processing HTTP requests.

Maintained by Jennifer Bryan. Last updated 2 years ago.

authentication google

113 stars 14.90 score 266 scripts 192 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

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

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

tidyverse

googlesheets4:Access Google Sheets using the Sheets API V4

Interact with Google Sheets through the Sheets API v4 <https://developers.google.com/sheets/api>. "API" is an acronym for "application programming interface"; the Sheets API allows users to interact with Google Sheets programmatically, instead of via a web browser. The "v4" refers to the fact that the Sheets API is currently at version 4. This package can read and write both the metadata and the cell data in a Sheet.

Maintained by Jennifer Bryan. Last updated 8 months ago.

google-drive google-sheets spreadsheet

363 stars 14.55 score 7.0k scripts 142 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

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

r-lib

pkgload:Simulate Package Installation and Attach

Simulates the process of installing a package and then attaching it. This is a key part of the 'devtools' package as it allows you to rapidly iterate while developing a package.

Maintained by Lionel Henry. Last updated 6 days ago.

59 stars 14.21 score 112 scripts 590 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

rstudio

pins:Pin, Discover, and Share Resources

Publish data sets, models, and other R objects, making it easy to share them across projects and with your colleagues. You can pin objects to a variety of "boards", including local folders (to share on a networked drive or with 'DropBox'), 'Posit Connect', 'AWS S3', and more.

Maintained by Julia Silge. Last updated 2 months ago.

azure gcloud rpins rsconnect s3 storage

321 stars 14.17 score 1.9k scripts 17 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

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

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

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

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

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

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

yulab-smu

scatterpie:Scatter Pie Plot

Creates scatterpie plots, especially useful for plotting pies on a map.

Maintained by Guangchuang Yu. Last updated 3 months ago.

62 stars 13.60 score 820 scripts 68 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

philchalmers

SimDesign:Structure for Organizing Monte Carlo Simulation Designs

Provides tools to safely and efficiently organize and execute Monte Carlo simulation experiments in R. The package controls the structure and back-end of Monte Carlo simulation experiments by utilizing a generate-analyse-summarise workflow. The workflow safeguards against common simulation coding issues, such as automatically re-simulating non-convergent results, prevents inadvertently overwriting simulation files, catches error and warning messages during execution, implicitly supports parallel processing with high-quality random number generation, and provides tools for managing high-performance computing (HPC) array jobs submitted to schedulers such as SLURM. For a pedagogical introduction to the package see Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.

Maintained by Phil Chalmers. Last updated 3 days ago.

monte-carlo-simulation simulation simulation-framework

62 stars 13.41 score 253 scripts 47 dependents

yulab-smu

tidytree:A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Maintained by Guangchuang Yu. Last updated 8 months ago.

phylogenetic-tree tidyverse tree-data

56 stars 13.36 score 584 scripts 128 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

guangchuangyu

ggplotify:Convert Plot to 'grob' or 'ggplot' Object

Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'ComplexHeatmap', 'eulerr', 'grid', 'lattice', 'magick', 'pheatmap', 'vcd' etc. by converting them to 'ggplot' objects.

Maintained by Guangchuang Yu. Last updated 1 years ago.

baseplot ggplot2 grid lattice upsetr vcd

108 stars 13.23 score 2.0k scripts 174 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

bioc

Spectra:Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Maintained by RforMassSpectrometry Package Maintainer. Last updated 24 days ago.

infrastructure proteomics massspectrometry metabolomics bioconductor hacktoberfest mass-spectrometry

41 stars 13.01 score 254 scripts 35 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

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

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

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

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

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-dbi

bigrquery:An Interface to Google's 'BigQuery' 'API'

Easily talk to Google's 'BigQuery' database from R.

Maintained by Hadley Wickham. Last updated 1 months ago.

bigquery database cpp

520 stars 12.47 score 1.8k scripts 4 dependents

ropensci

treeio:Base Classes and Functions for Phylogenetic Tree Input and Output

'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.

Maintained by Guangchuang Yu. Last updated 5 months ago.

software annotation clustering dataimport datarepresentation alignment multiplesequencealignment phylogenetics exporter parser phylogenetic-trees

102 stars 12.46 score 1.3k scripts 122 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

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

gaospecial

ggVennDiagram:A 'ggplot2' Implement of Venn Diagram

Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality. 'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in four components, set edges/labels, and region edges/labels. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar. From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when number of sets is more than 7.

Maintained by Chun-Hui Gao. Last updated 5 months ago.

set-operations upset upsetplot venn-diagram venn-plot

292 stars 12.31 score 1.3k scripts 4 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

yulab-smu

aplot:Decorate a 'ggplot' with Associated Information

For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. Inspired by the 'Method 2' in 'ggtree' (G Yu (2018) <doi:10.1093/molbev/msy194>), 'aplot' provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.

Maintained by Guangchuang Yu. Last updated 1 months ago.

103 stars 12.25 score 520 scripts 118 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

openpharma

mmrm:Mixed Models for Repeated Measures

Mixed models for repeated measures (MMRM) are a popular choice for analyzing longitudinal continuous outcomes in randomized clinical trials and beyond; see Cnaan, Laird and Slasor (1997) <doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E> for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso (2008) <doi:10.1177/009286150804200402> for a review. This package implements MMRM based on the marginal linear model without random effects using Template Model Builder ('TMB') which enables fast and robust model fitting. Users can specify a variety of covariance matrices, weight observations, fit models with restricted or standard maximum likelihood inference, perform hypothesis testing with Satterthwaite or Kenward-Roger adjustment, and extract least square means estimates by using 'emmeans'.

Maintained by Daniel Sabanes Bove. Last updated 24 days ago.

cpp

138 stars 12.15 score 113 scripts 4 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

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

pecanproject

PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis

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 goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 8 hours ago.

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

216 stars 11.91 score 127 scripts 27 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

guangchuangyu

hexSticker:Create Hexagon Sticker in R

Helper functions for creating reproducible hexagon sticker purely in R.

Maintained by Guangchuang Yu. Last updated 2 months ago.

ggplot2 hexagon-sticker logo stickers visualization

773 stars 11.79 score 1.3k scripts 8 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

kevinushey

sourcetools:Tools for Reading, Tokenizing and Parsing R Code

Tools for Reading, Tokenizing and Parsing R Code.

Maintained by Kevin Ushey. Last updated 2 years ago.

cpp

78 stars 11.77 score 32 scripts 1.8k 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

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 8 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

r-lib

mockery:Mocking Library for R

The two main functionalities of this package are creating mock objects (functions) and selectively intercepting calls to a given function that originate in some other function. It can be used with any testing framework available for R. Mock objects can be injected with either this package's own stub() function or a similar with_mock() facility present in the 'testthat' package.

Maintained by Hadley Wickham. Last updated 1 years ago.

100 stars 11.57 score 504 scripts 5 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

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 4 days ago.

microbiome software dataimport analysis bioconductor cpp

51 stars 11.51 score 316 scripts 5 dependents

r-lib

gmailr:Access the 'Gmail' 'RESTful' API

An interface to the 'Gmail' 'RESTful' API. Allows access to your 'Gmail' messages, threads, drafts and labels.

Maintained by Jennifer Bryan. Last updated 1 years ago.

230 stars 11.50 score 289 scripts 1 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 18 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

mllg

batchtools:Tools for Computation on Batch Systems

As a successor of the packages 'BatchJobs' and 'BatchExperiments', this package provides a parallel implementation of the Map function for high performance computing systems managed by schedulers 'IBM Spectrum LSF' (<https://www.ibm.com/products/hpc-workload-management>), 'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>), 'TORQUE/PBS' (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>), or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>). A multicore and socket mode allow the parallelization on a local machines, and multiple machines can be hooked up via SSH to create a makeshift cluster. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.

Maintained by Michel Lang. Last updated 2 years ago.

batchexperiments batchjobs docker-swarm high-performance-computing hpc hpc-clusters lsf openlava parallel-computing reproducibility sge slurm torque

175 stars 11.39 score 772 scripts 14 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

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 19 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

ropensci

tarchetypes:Archetypes for Targets

Function-oriented Make-like declarative pipelines for Statistics and data science are supported in the 'targets' R package. As an extension to 'targets', the 'tarchetypes' package provides convenient user-side functions to make 'targets' easier to use. By establishing reusable archetypes for common kinds of targets and pipelines, these functions help express complicated reproducible pipelines concisely and compactly. The methods in this package were influenced by the 'targets' R package. by Will Landau (2018) <doi:10.21105/joss.00550>.

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

data-science high-performance-computing peer-reviewed pipeline r-targetopia reproducibility targets workflow

142 stars 11.27 score 1.7k scripts 10 dependents

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

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

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

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

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

guangchuangyu

ggimage:Use Image in 'ggplot2'

Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.

Maintained by Guangchuang Yu. Last updated 1 years ago.

ggplot2 image visualization

172 stars 11.12 score 2.4k scripts 20 dependents

jgx65

hierfstat:Estimation and Tests of Hierarchical F-Statistics

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

Maintained by Jerome Goudet. Last updated 4 months ago.

devtools fstatistics gwas hierfstat kinship population-genetics population-genomics quantitative-genetics simulations

25 stars 11.06 score 560 scripts 5 dependents

choonghyunryu

dlookr:Tools for Data Diagnosis, Exploration, Transformation

A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values, outliers, and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and the relationship between the target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputes missing values and outliers, and resolves skewness. And it creates automated reports that support these three tasks.

Maintained by Choonghyun Ryu. Last updated 10 months ago.

212 stars 11.05 score 748 scripts 2 dependents

mhahsler

arulesViz:Visualizing Association Rules and Frequent Itemsets

Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration. Michael Hahsler (2017) <doi:10.32614/RJ-2017-047>.

Maintained by Michael Hahsler. Last updated 7 months ago.

arules association-rules frequent-itemsets interactive-visualizations visualization

54 stars 11.03 score 1.7k scripts 2 dependents

pik-piam

madrat:May All Data be Reproducible and Transparent (MADRaT) *

Provides a framework which should improve reproducibility and transparency in data processing. It provides functionality such as automatic meta data creation and management, rudimentary quality management, data caching, work-flow management and data aggregation. * The title is a wish not a promise. By no means we expect this package to deliver everything what is needed to achieve full reproducibility and transparency, but we believe that it supports efforts in this direction.

Maintained by Jan Philipp Dietrich. Last updated 11 days ago.

15 stars 11.03 score 83 scripts 38 dependents

gdemin

expss:Tables, Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics

Package computes and displays tables with support for 'SPSS'-style labels, multiple and nested banners, weights, multiple-response variables and significance testing. There are facilities for nice output of tables in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods for labelled variables add value labels support to base R functions and to some functions from other packages. Additionally, the package brings popular data transformation functions from 'SPSS' Statistics and 'Excel': 'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc. These functions are very useful for data processing in marketing research surveys. Package intended to help people to move data processing from 'Excel' and 'SPSS' to R.

Maintained by Gregory Demin. Last updated 12 months ago.

excel labels labels-support msexcel pivot-tables recode spss spss-statistics tables variable-labels vlookup

84 stars 11.00 score 1.8k scripts 4 dependents

sachsmc

plotROC:Generate Useful ROC Curve Charts for Print and Interactive Use

Most ROC curve plots obscure the cutoff values and inhibit interpretation and comparison of multiple curves. This attempts to address those shortcomings by providing plotting and interactive tools. Functions are provided to generate an interactive ROC curve plot for web use, and print versions. A Shiny application implementing the functions is also included.

Maintained by Michael C. Sachs. Last updated 5 months ago.

87 stars 10.93 score 932 scripts 7 dependents

davidgohel

officedown:Enhanced 'R Markdown' Format for 'Word' and 'PowerPoint'

Allows production of 'Microsoft' corporate documents from 'R Markdown' by reusing formatting defined in 'Microsoft Word' documents. You can reuse table styles, list styles but also add column sections, landscape oriented pages. Table and image captions as well as cross-references are transformed into 'Microsoft Word' fields, allowing documents edition and merging without issue with references; the syntax conforms to the 'bookdown' cross-reference definition. Objects generated by the 'officer' package are also supported in the 'knitr' chunks. 'Microsoft PowerPoint' presentations also benefit from this as well as the ability to produce editable vector graphics in 'PowerPoint' and also to define placeholder where content is to be added.

Maintained by David Gohel. Last updated 13 days ago.

371 stars 10.93 score 342 scripts 7 dependents

bioc

infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data

Using single-cell RNA-Seq expression to visualize CNV in cells.

Maintained by Christophe Georgescu. Last updated 5 months ago.

software copynumbervariation variantdetection structuralvariation genomicvariation genetics transcriptomics statisticalmethod bayesian hiddenmarkovmodel singlecell jags cpp

601 stars 10.92 score 674 scripts

tylermorganwall

rayrender:Build and Raytrace 3D Scenes

Render scenes using pathtracing. Build 3D scenes out of spheres, cubes, planes, disks, triangles, cones, curves, line segments, cylinders, ellipsoids, and 3D models in the 'Wavefront' OBJ file format or the PLY Polygon File Format. Supports several material types, textures, multicore rendering, and tone-mapping. Based on the "Ray Tracing in One Weekend" book series. Peter Shirley (2018) <https://raytracing.github.io>.

Maintained by Tyler Morgan-Wall. Last updated 4 days ago.

libx11 cpp

631 stars 10.87 score 188 scripts 8 dependents

marce10

warbleR:Streamline Bioacoustic Analysis

Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.

Maintained by Marcelo Araya-Salas. Last updated 2 months ago.

animal-acoustic-signals audio-processing bioacoustics spectrogram streamline-analysis cpp

56 stars 10.86 score 270 scripts 4 dependents

michelnivard

gptstudio:Use Large Language Models Directly in your Development Environment

Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.

Maintained by James Wade. Last updated 5 days ago.

chatgpt gpt-3 rstudio rstudio-addin

930 stars 10.85 score 43 scripts 1 dependents

r-lib

vdiffr:Visual Regression Testing and Graphical Diffing

An extension to the 'testthat' package that makes it easy to add graphical unit tests. It provides a Shiny application to manage the test cases.

Maintained by Lionel Henry. Last updated 5 months ago.

ggplot2 graphics testthat libpng cpp

191 stars 10.84 score 254 scripts 5 dependents

grunwaldlab

poppr:Genetic Analysis of Populations with Mixed Reproduction

Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the 'adegenet' package. Originally described in Kamvar, Tabima, and Grünwald (2014) <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and Grünwald (2015) <doi:10.3389/fgene.2015.00208>.

Maintained by Zhian N. Kamvar. Last updated 11 months ago.

clonality genetic-analysis genetic-distances minimum-spanning-networks multilocus-genotypes multilocus-lineages population-genetics populations openmp

69 stars 10.84 score 672 scripts

moodymudskipper

flow:View and Browse Code Using Flow Diagrams

Visualize as flow diagrams the logic of functions, expressions or scripts in a static way or when running a call, visualize the dependencies between functions or between modules in a shiny app, and more.

Maintained by Antoine Fabri. Last updated 4 months ago.

405 stars 10.84 score 61 scripts

yang-tang

shinyjqui:'jQuery UI' Interactions and Effects for Shiny

An extension to shiny that brings interactions and animation effects from 'jQuery UI' library.

Maintained by Yang Tang. Last updated 1 years ago.

jquery-ui shiny

276 stars 10.83 score 464 scripts 19 dependents

bioc

ANCOMBC:Microbiome differential abudance and correlation analyses with bias correction

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

Maintained by Huang Lin. Last updated 15 days ago.

differentialexpression microbiome normalization sequencing software ancom ancombc ancombc2 correlation differential-abundance-analysis secom

120 stars 10.79 score 406 scripts 1 dependents

mitchelloharawild

vitae:Curriculum Vitae for R Markdown

Provides templates and functions to simplify the production and maintenance of curriculum vitae.

Maintained by Mitchell OHara-Wild. Last updated 10 months ago.

cv ozunconf18 resume unconf

1.2k stars 10.78 score 556 scripts

ovvo-financial

NNS:Nonlinear Nonparametric Statistics

Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).

Maintained by Fred Viole. Last updated 3 days ago.

clustering econometrics machine-learning nonlinear nonparametric partial-moments statistics time-series cpp

72 stars 10.77 score 66 scripts 3 dependents

pecanproject

PEcAn.benchmark:PEcAn Functions Used for Benchmarking

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 goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. The PEcAn.benchmark package provides utilities for comparing models and data, including a suite of statistical metrics and plots.

Maintained by Mike Dietze. Last updated 8 hours ago.

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

216 stars 10.73 score 416 scripts 11 dependents

htmlwidgets

sparkline:'jQuery' Sparkline 'htmlwidget'

Include interactive sparkline charts <http://omnipotent.net/jquery.sparkline> in all R contexts with the convenience of 'htmlwidgets'.

Maintained by Ramnath Vaidyanathan. Last updated 6 years ago.

245 stars 10.73 score 556 scripts 5 dependents

rstudio

pointblank:Data Validation and Organization of Metadata for Local and Remote Tables

Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.

Maintained by Richard Iannone. Last updated 5 days ago.

data-assertions data-checker data-dictionaries data-frames data-inference data-management data-profiler data-quality data-validation data-verification database-tables easy-to-understand reporting-tool schema-validation testing-tools yaml-configuration

942 stars 10.73 score 284 scripts

sachaepskamp

semPlot:Path Diagrams and Visual Analysis of Various SEM Packages' Output

Path diagrams and visual analysis of various SEM packages' output.

Maintained by Sacha Epskamp. Last updated 3 years ago.

63 stars 10.64 score 2.1k scripts 13 dependents

r-spatial

leafgl:High-Performance 'WebGl' Rendering for Package 'leaflet'

Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript library to render large data in the browser using 'WebGl'.

Maintained by Tim Appelhans. Last updated 5 months ago.

271 stars 10.63 score 157 scripts 27 dependents

merlinoa

shinyFeedback:Display User Feedback in Shiny Apps

Easily display user feedback in Shiny apps.

Maintained by Andy Merlino. Last updated 3 years ago.

feedback shiny shiny-inputs

191 stars 10.62 score 209 scripts 16 dependents

hrbrmstr

waffle:Create Waffle Chart Visualizations

Square pie charts (a.k.a. waffle charts) can be used to communicate parts of a whole for categorical quantities. To emulate the percentage view of a pie chart, a 10x10 grid should be used with each square representing 1% of the total. Modern uses of waffle charts do not necessarily adhere to this rule and can be created with a grid of any rectangular shape. Best practices suggest keeping the number of categories small, just as should be done when creating pie charts. Tools are provided to create waffle charts as well as stitch them together, and to use glyphs for making isotype pictograms.

Maintained by Bob Rudis. Last updated 2 years ago.

data-visualisation data-visualization datavisualization ggplot2 square-pie-charts waffle-charts

777 stars 10.62 score 1.3k scripts 5 dependents

business-science

modeltime:The Tidymodels Extension for Time Series Modeling

The time series forecasting framework for use with the 'tidymodels' ecosystem. Models include ARIMA, Exponential Smoothing, and additional time series models from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition" (<https://otexts.com/fpp2/>). Refer to "Prophet: forecasting at scale" (<https://research.facebook.com/blog/2017/02/prophet-forecasting-at-scale/>.).

Maintained by Matt Dancho. Last updated 5 months ago.

arima data-science deep-learning ets forecasting machine-learning machine-learning-algorithms modeltime prophet tbats tidymodeling tidymodels time time-series time-series-analysis timeseries timeseries-forecasting

551 stars 10.61 score 1.1k scripts 7 dependents

predictiveecology

SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 1 months ago.

discrete-events-simulations simulation-framework simulation-modeling

10 stars 10.61 score 142 scripts 6 dependents

bioc

Glimma:Interactive visualizations for gene expression analysis

This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.

Maintained by Shian Su. Last updated 2 months ago.

differentialexpression geneexpression microarray reportwriting rnaseq sequencing visualization differential-expression interactive-visualizations

32 stars 10.58 score 600 scripts 1 dependents

bioc

ORFik:Open Reading Frames in Genomics

R package for analysis of transcript and translation features through manipulation of sequence data and NGS data like Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in the sense that any transcript region can be analysed, as the name hints to it was made with investigation of ribosomal patterns over Open Reading Frames (ORFs) as it's primary use case. ORFik is extremely fast through use of C++, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CAGE-Seq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for whole genomes and much more.

Maintained by Haakon Tjeldnes. Last updated 1 months ago.

immunooncology software sequencing riboseq rnaseq functionalgenomics coverage alignment dataimport cpp

33 stars 10.56 score 115 scripts 2 dependents

yulab-smu

ggfun:Miscellaneous Functions for 'ggplot2'

Useful functions and utilities for 'ggplot' object (e.g., geometric layers, themes, and utilities to edit the object).

Maintained by Guangchuang Yu. Last updated 14 days ago.

18 stars 10.53 score 58 scripts 152 dependents

caseyyoungflesh

MCMCvis:Tools to Visualize, Manipulate, and Summarize MCMC Output

Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with Stan, NIMBLE, JAGS, and other software.

Maintained by Casey Youngflesh. Last updated 4 months ago.

38 stars 10.52 score 1.8k scripts 5 dependents

predictiveecology

reproducible:Enhance Reproducibility of R Code

A collection of high-level, machine- and OS-independent tools for making reproducible and reusable content in R. The two workhorse functions are Cache() and prepInputs(). Cache() allows for nested caching, is robust to environments and objects with environments (like functions), and deals with some classes of file-backed R objects e.g., from terra and raster packages. Both functions have been developed to be foundational components of data retrieval and processing in continuous workflow situations. In both functions, efforts are made to make the first and subsequent calls of functions have the same result, but faster at subsequent times by way of checksums and digesting. Several features are still under development, including cloud storage of cached objects allowing for sharing between users. Several advanced options are available, see ?reproducibleOptions().

Maintained by Eliot J B McIntire. Last updated 2 months ago.

reproducibility reproducible-research

41 stars 10.52 score 122 scripts 15 dependents