Showing 200 of total 407 results (show query)
r-lib
devtools:Tools to Make Developing R Packages Easier
Collection of package development tools.
Maintained by Jennifer Bryan. Last updated 6 months ago.
2.4k stars 19.55 score 51k scripts 150 dependentsr-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.
869 stars 17.54 score 5.6k scripts 336 dependentsr-lib
gh:'GitHub' 'API'
Minimal client to access the 'GitHub' 'API'.
Maintained by Gábor Csárdi. Last updated 2 months ago.
224 stars 15.55 score 444 scripts 401 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-storegit-lfspeer-reviewed
187 stars 12.98 score 187 scripts 12 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.
fisheriesfisheries-stock-assessmentstock-synthesis
43 stars 11.38 score 1.0k scripts 2 dependents
r-hub
rhub:Tools for R Package Developers
R-hub v2 uses GitHub Actions to run 'R CMD check' and similar package checks. The 'rhub' package helps you set up R-hub v2 for your R package, and start running checks.
Maintained by Gábor Csárdi. Last updated 24 days ago.
359 stars 11.33 score 191 scripts 1 dependents
dslc-io
tidytuesdayR:Access the Weekly 'TidyTuesday' Project Dataset
'TidyTuesday' is a project by the 'Data Science Learning Community' in which they post a weekly dataset in a public data repository (<https://github.com/rfordatascience/tidytuesday>) for people to analyze and visualize. This package provides the tools to easily download this data and the description of the source.
Maintained by Jon Harmon. Last updated 5 days ago.
77 stars 10.13 score 3.0k scripts
8-bit-sheep
googleAnalyticsR:Google Analytics API into R
Interact with the Google Analytics APIs <https://developers.google.com/analytics/>, including the Core Reporting API (v3 and v4), Management API, User Activity API GA4's Data API and Admin API and Multi-Channel Funnel API.
Maintained by Erik Grönroos. Last updated 7 months ago.
analyticsapigooglegoogleanalyticsrgoogleauthr
262 stars 10.11 score 680 scripts 1 dependentsr-lib
ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More
Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.
Maintained by Malcolm Barrett. Last updated 3 years ago.
165 stars 9.92 score 196 scripts 14 dependents
cjvanlissa
worcs:Workflow for Open Reproducible Code in Science
Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.
Maintained by Caspar J. Van Lissa. Last updated 2 days ago.
83 stars 9.77 score 59 scripts 1 dependents
thinkr-open
fusen:Build a Package from Rmarkdown Files
Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.
Maintained by Vincent Guyader. Last updated 2 months ago.
163 stars 9.45 score 35 scriptsropensci
DataPackageR:Construct Reproducible Analytic Data Sets as R Packages
A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.
Maintained by Dave Slager. Last updated 7 months ago.
156 stars 9.38 score 72 scripts
r-spatial
link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools
Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.
Maintained by Chris Reudenbach. Last updated 4 months ago.
26 stars 8.99 score 78 scripts 1 dependents
pharmar
riskmetric:Risk Metrics to Evaluating R Packages
Facilities for assessing R packages against a number of metrics to help quantify their robustness.
Maintained by Eli Miller. Last updated 7 days ago.
166 stars 8.98 score 43 scripts
cjbarrie
academictwitteR:Access the Twitter Academic Research Product Track V2 API Endpoint
Package to query the Twitter Academic Research Product Track, providing access to full-archive search and other v2 API endpoints. Functions are written with academic research in mind. They provide flexibility in how the user wishes to store collected data, and encourage regular storage of data to mitigate loss when collecting large volumes of tweets. They also provide workarounds to manage and reshape the format in which data is provided on the client side.
Maintained by Christopher Barrie. Last updated 2 years ago.
275 stars 8.94 score 177 scripts
guangchuangyu
badger:Badge for R Package
Query information and generate badge for using in README and GitHub Pages.
Maintained by Guangchuang Yu. Last updated 9 months ago.
197 stars 8.92 score 225 scripts 5 dependents
ajrgodfrey
BrailleR:Improved Access for Blind Users
Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.
123 stars 8.90 score 143 scriptsropensci
codemetar:Generate 'CodeMeta' Metadata for R Packages
The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
Maintained by Carl Boettiger. Last updated 2 months ago.
metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed
68 stars 8.90 score 34 scripts 6 dependents
pik-piam
remind2:The REMIND R package (2nd generation)
Contains the REMIND-specific routines for data and model output manipulation.
Maintained by Renato Rodrigues. Last updated 3 days ago.
8.87 score 161 scripts 5 dependents
dmi3kno
polite:Be Nice on the Web
Be responsible when scraping data from websites by following polite principles: introduce yourself, ask for permission, take slowly and never ask twice.
Maintained by Dmytro Perepolkin. Last updated 2 years ago.
crawlermemoiserate-limiterrobotstxtrvestscraperwebscraping
327 stars 8.86 score 596 scripts 5 dependents
cynkra
fledge:Smoother Change Tracking and Versioning for R Packages
Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.
Maintained by Kirill Müller. Last updated 3 months ago.
188 stars 8.73 score 10 scripts
ss3sim
ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis
A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.
Maintained by Kelli F. Johnson. Last updated 5 months ago.
fisheriessimulationstock-synthesis
39 stars 8.72 score 149 scripts
bioc
memes:motif matching, comparison, and de novo discovery using the MEME Suite
A seamless interface to the MEME Suite family of tools for motif analysis. 'memes' provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. 'memes' functions and data structures are amenable to both base R and tidyverse workflows.
Maintained by Spencer Nystrom. Last updated 5 months ago.
dataimportfunctionalgenomicsgeneregulationmotifannotationmotifdiscoverysequencematchingsoftware
50 stars 8.69 score 117 scripts 1 dependents
helske
seqHMM:Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series
Designed for estimating variants of hidden (latent) Markov models (HMMs), mixture HMMs, and non-homogeneous HMMs (NHMMs) for social sequence data and other categorical time series. Special cases include feedback-augmented NHMMs, Markov models without latent layer, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models as well as initial, transition and emission probabilities in NHMMs. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and HMMs. For NHMMs, there are also methods for computing average causal effects and marginal state and emission probabilities. Models are estimated using maximum likelihood via the EM algorithm or direct numerical maximization with analytical gradients. Documentation is available via several vignettes, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>). For methodology behind the NHMMs, see Helske (2025, <doi:arXiv:2503.16014>)
Maintained by Jouni Helske. Last updated 1 hours ago.
categorical-dataem-algorithmhidden-markov-modelshmmmixture-markov-modelstime-seriesopenblascppopenmp
98 stars 8.51 score 92 scripts 1 dependents
posit-dev
shinylive:Run 'shiny' Applications in the Browser
Exporting 'shiny' applications with 'shinylive' allows you to run them entirely in a web browser, without the need for a separate R server. The traditional way of deploying 'shiny' applications involves in a separate server and client: the server runs R and 'shiny', and clients connect via the web browser. When an application is deployed with 'shinylive', R and 'shiny' run in the web browser (via 'webR'): the browser is effectively both the client and server for the application. This allows for your 'shiny' application exported by 'shinylive' to be hosted by a static web server.
Maintained by Barret Schloerke. Last updated 5 months ago.
187 stars 8.35 score 194 scripts
ramikrispin
coronavirus:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Maintained by Rami Krispin. Last updated 2 years ago.
covid-19covid19covid19-datadataset
499 stars 8.25 score 716 scripts
mazamascience
MazamaSpatialUtils:Spatial Data Download and Utility Functions
A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)
Maintained by Jonathan Callahan. Last updated 5 months ago.
5 stars 8.01 score 282 scripts 2 dependentsbioc
biocthis:Automate package and project setup for Bioconductor packages
This package expands the usethis package with the goal of helping automate the process of creating R packages for Bioconductor or making them Bioconductor-friendly.
Maintained by Leonardo Collado-Torres. Last updated 10 days ago.
softwarereportwritingactionsbioconductorbiocthisgithubstylerusethis
51 stars 7.90 score 4 scripts 1 dependents
matloff
dsld:Data Science Looks at Discrimination
Statistical and graphical tools for detecting and measuring discrimination and bias, be it racial, gender, age or other. Detection and remediation of bias in machine learning algorithms. 'Python' interfaces available.
Maintained by Norm Matloff. Last updated 2 months ago.
12 stars 7.81 score 35 scriptsmazamascience
MazamaCoreUtils:Utility Functions for Production R Code
A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, cache management and date-time parsing. Functions for date-time parsing and formatting require that time zones be specified explicitly, avoiding a common source of error when working with environmental time series.
Maintained by Jonathan Callahan. Last updated 4 months ago.
4 stars 7.76 score 119 scripts 5 dependents
cmu-delphi
epidatr:Client for Delphi's 'Epidata' API
The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.
Maintained by David Weber. Last updated 11 days ago.
5 stars 7.71 score 114 scripts
carpentries
sandpaper:Create and Curate Carpentries Lessons
We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.
Maintained by Robert Davey. Last updated 2 months ago.
carpentriescarpentries-infrastructurecarpentries-workbenchlesson-templatelessonsmarkdownstatic-site-generator
44 stars 7.68 score 8 scriptsbioc
BiocPkgTools:Collection of simple tools for learning about Bioconductor Packages
Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.
Maintained by Sean Davis. Last updated 27 days ago.
softwareinfrastructurebioconductormetadata
21 stars 7.67 score 68 scripts
neurogenomics
rworkflows:Test, Document, Containerise, and Deploy R Packages
Reproducibility is essential to the progress of research, yet achieving it remains elusive even in computational fields. Continuous Integration (CI) platforms offer a powerful way to launch automated workflows to check and document code, but often require considerable time, effort, and technical expertise to setup. We therefore developed the rworkflows suite to make robust CI workflows easy and freely accessible to all R package developers. rworkflows consists of 1) a CRAN/Bioconductor-compatible R package template, 2) an R package to quickly implement a standardised workflow, and 3) a centrally maintained GitHub Action.
Maintained by Brian Schilder. Last updated 2 months ago.
softwareworkflowmanagementbioconductorcontainerscontinuous-integrationdockerdockerhubgithub-actionsreproducibilityworkflows
79 stars 7.60 score 6 scriptsropensci
tic:Tasks Integrating Continuously: CI-Agnostic Workflow Definitions
Provides a way to describe common build and deployment workflows for R-based projects: packages, websites (e.g. blogdown, pkgdown), or data processing (e.g. research compendia). The recipe is described independent of the continuous integration tool used for processing the workflow (e.g. 'GitHub Actions' or 'Circle CI'). This package has been peer-reviewed by rOpenSci (v0.3.0.9004).
Maintained by Eli Miller. Last updated 2 months ago.
appveyorcontinuous-integrationdeploymentgithubactionstravis-ci
155 stars 7.57 score 16 scripts
ropensci
allcontributors:Acknowledge all Contributors to a Project
Acknowledge all contributors to a project via a single function call. The function appends to a 'README' or other specified file(s) a table with names of all individuals who contributed via code or repository issues. The package also includes several additional functions to extract and quantify contributions to any repository.
Maintained by Mark Padgham. Last updated 30 days ago.
29 stars 7.46 score 5 scripts 1 dependentsbioc
cogena:co-expressed gene-set enrichment analysis
cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.
Maintained by Zhilong Jia. Last updated 5 months ago.
clusteringgenesetenrichmentgeneexpressionvisualizationpathwayskegggomicroarraysequencingsystemsbiologydatarepresentationdataimportbioconductorbioinformatics
12 stars 7.36 score 32 scripts
rundel
ghclass:Tools for Managing Classes on GitHub
Interface for the GitHub API that enables efficient management of courses on GitHub. It has a functionality for managing organizations, teams, repositories, and users on GitHub and helps automate most of the tedious and repetitive tasks around creating and distributing assignments.
Maintained by Colin Rundel. Last updated 2 months ago.
142 stars 7.32 score 70 scripts
hoxo-m
githubinstall:A Helpful Way to Install R Packages Hosted on GitHub
Provides an helpful way to install packages hosted on GitHub.
Maintained by Koji Makiyama. Last updated 7 years ago.
49 stars 7.29 score 177 scripts
inbo
checklist:A Thorough and Strict Set of Checks for R Packages and Source Code
An opinionated set of rules for R packages and R source code projects.
Maintained by Thierry Onkelinx. Last updated 1 months ago.
checklistcontinuous-integrationcontinuous-testingquality-assurance
19 stars 7.24 score 21 scripts 2 dependents
hubverse-org
hubUtils:Core 'hubverse' Utilities
Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> for an overview of Collaborative Hubs.
Maintained by Anna Krystalli. Last updated 19 days ago.
6 stars 7.22 score 49 scripts 7 dependentspik-piam
lucode2:Code Manipulation and Analysis Tools
A collection of tools which allow to manipulate and analyze code.
Maintained by Jan Philipp Dietrich. Last updated 10 days ago.
7.22 score 364 scripts 8 dependents
usaid-oha-si
glamr:SI Utilities Package
Provides a series of base functions useful to the GH OHA SI team. This includes project setup, pulling from DATIM, and key functions for working with the MSD.
Maintained by Aaron Chafetz. Last updated 6 months ago.
2 stars 7.20 score 1.3k scripts 1 dependents
beanumber
etl:Extract-Transform-Load Framework for Medium Data
A predictable and pipeable framework for performing ETL (extract-transform-load) operations on publicly-accessible medium-sized data set. This package sets up the method structure and implements generic functions. Packages that depend on this package download specific data sets from the Internet, clean them up, and import them into a local or remote relational database management system.
Maintained by Benjamin S. Baumer. Last updated 1 years ago.
129 stars 7.17 score 38 scripts 1 dependents
rladies
meetupr:Meetup R API
Provides access to data from <https:www.meetup.com> (see <https:www.meetup.com/meetup_api/> for more information).
Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.
apiapi-wrappermeetupr-ladiesrladiesrladies-global
77 stars 7.03 score 92 scripts
permaverse
flipr:Flexible Inference via Permutations in R
A flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing, on any kind of data, be it univariate, multivariate, or more complex such as network-valued data, topological data, functional data or density-valued data.
Maintained by Aymeric Stamm. Last updated 12 days ago.
6 stars 7.02 score 24 scripts 1 dependentsr-lib
roxygen2md:'Roxygen' to 'Markdown'
Converts elements of 'roxygen' documentation to 'markdown'.
Maintained by Kirill Müller. Last updated 4 months ago.
68 stars 7.00 score 11 scripts 2 dependentsthinkr-open
thinkr:Tools for Cleaning Up Messy Files
Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
Maintained by Vincent Guyader. Last updated 3 years ago.
hacktoberfestthinkr-not-maintained
29 stars 6.96 score 45 scripts
sportsdataverse
hoopR:Access Men's Basketball Play by Play Data
A utility to quickly obtain clean and tidy men's basketball play by play data. Provides functions to access live play by play and box score data from ESPN<https://www.espn.com> with shot locations when available. It is also a full NBA Stats API<https://www.nba.com/stats/> wrapper. It is also a scraping and aggregating interface for Ken Pomeroy's men's college basketball statistics website<https://kenpom.com>. It provides users with an active subscription the capability to scrape the website tables and analyze the data for themselves.
Maintained by Saiem Gilani. Last updated 1 years ago.
basketballcollege-basketballespnkenpomnbanba-analyticsnba-apinba-datanba-statisticsnba-statsnba-stats-apincaancaa-basketballncaa-bracketncaa-playersncaa-ratingsncaamsportsdataverse
91 stars 6.93 score 261 scripts
dfe-analytical-services
dfeR:Common Department for Education Analysis Tasks
Preferred methods for common analytical tasks that are undertaken across the Department, including number formatting, project templates and curated reference data.
Maintained by Cam Race. Last updated 1 months ago.
12 stars 6.89 score 8 scriptspik-piam
edgeTransport:Prepare EDGE Transport Data for the REMIND model
EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation with a high level of detail in its representation of technological and modal options. It is a partial equilibrium model with a nested multinomial logit structure and relies on the modified logit formulation. Most of the sources are not publicly available. PIK-internal users can find the sources in the distributed file system in the folder `/p/projects/rd3mod/inputdata/sources/EDGE-Transport-Standalone`.
Maintained by Johanna Hoppe. Last updated 2 days ago.
5 stars 6.84 score 16 scripts 2 dependents
raymondbalise
rUM:R Templates from the University of Miami
This holds some r markdown and quarto templates and a template to create a research project in "R Studio".
Maintained by Raymond Balise. Last updated 10 days ago.
9 stars 6.84 score 16 scripts
ready4-dev
ready4:Develop and Use Modular Health Economic Models
A template model module, tools to help find model modules derived from this template and a programming syntax to use these modules in health economic analyses. These elements are the foundation for a prototype software framework for developing living and transferable models and using those models in reproducible health economic analyses. The software framework is extended by other R libraries. For detailed documentation about the framework and how to use it visit <https://www.ready4-dev.com/>. For a background to the methodological issues that the framework is attempting to help solve, see Hamilton et al. (2024) <doi:10.1007/s40273-024-01378-8>.
Maintained by Matthew Hamilton. Last updated 5 months ago.
computational-modelinghealth-economicssoftware-framework
2 stars 6.84 score 95 scripts
kozodoi
fairness:Algorithmic Fairness Metrics
Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.
Maintained by Nikita Kozodoi. Last updated 2 years ago.
algorithmic-discriminationalgorithmic-fairnessdiscriminationdisparate-impactfairnessfairness-aifairness-mlmachine-learning
32 stars 6.82 score 69 scripts 1 dependents
emilyriederer
projmgr:Task Tracking and Project Management with GitHub
Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.
Maintained by Emily Riederer. Last updated 1 years ago.
124 stars 6.81 score 34 scripts 5 dependentsthinkr-open
checkhelper:Deal with Check Outputs
Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.
Maintained by Sebastien Rochette. Last updated 1 years ago.
34 stars 6.74 score 18 scripts
frbcesab
rcompendium:Create a Package or Research Compendium Structure
Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.
Maintained by Nicolas Casajus. Last updated 2 months ago.
reproducible-researchresearch-compendium
40 stars 6.72 score 22 scripts
ropengov
sorvi:Functions for Finnish Open Data
Misc support functions for rOpenGov and open data downloads.
Maintained by Leo Lahti. Last updated 1 years ago.
13 stars 6.71 score 131 scripts
correlaid
newsanchor:Client for the News API
Interface to gather news from the 'News API', based on a multilevel query <https://newsapi.org/>. A personal API key is required.
Maintained by Yannik Buhl. Last updated 5 years ago.
36 stars 6.70 score 40 scriptsbioc
megadepth:megadepth: BigWig and BAM related utilities
This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.
Maintained by David Zhang. Last updated 4 months ago.
softwarecoveragedataimporttranscriptomicsrnaseqpreprocessingbambigwigdasptermegadepthrecount2recount3
12 stars 6.69 score 7 scripts 3 dependents
kylegrealis
froggeR:Enhance 'Quarto' Project Workflows and Standards
Streamlines 'Quarto' workflows by providing tools for consistent project setup and documentation. Enables portability through reusable metadata, automated project structure creation, and standardized templates. Features include enhanced project initialization, pre-formatted 'Quarto' documents, comprehensive data protection settings, custom styling, and structured documentation generation. Designed to improve efficiency and collaboration in R data science projects by reducing repetitive setup tasks while maintaining consistent formatting across multiple documents. There are many valuable resources providing in-depth explanations of customizing 'Quarto' templates and theme styling by the Posit team: <https://quarto.org/docs/output-formats/html-themes.html#customizing-themes> & <https://quarto.org/docs/output-formats/html-themes-more.html>, and at the Bootstrap community's GitHub at <https://github.com/twbs/bootstrap/blob/main/scss/_variables.scss>.
Maintained by Kyle Grealis. Last updated 15 days ago.
data-scienceproject-managementquarto
26 stars 6.67 score 6 scripts
rorynolan
exampletestr:Help for Writing Unit Tests Based on Function Examples
Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package. Sort of like python 'doctests' for R.
Maintained by Rory Nolan. Last updated 6 months ago.
37 stars 6.63 score 8 scriptsmazamascience
AirMonitor:Air Quality Data Analysis
Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://document.airnow.gov/technical-assistance-document-for-the-reporting-of-daily-air-quailty.pdf>.
Maintained by Jonathan Callahan. Last updated 6 months ago.
7 stars 6.57 score 178 scripts
jakesherman
easypackages:Easy Loading and Installing of Packages
Easily load and install multiple packages from different sources, including CRAN and GitHub. The libraries function allows you to load or attach multiple packages in the same function call. The packages function will load one or more packages, and install any packages that are not installed on your system (after prompting you). Also included is a from_import function that allows you to import specific functions from a package into the global environment.
Maintained by Jake Sherman. Last updated 7 years ago.
11 stars 6.52 score 490 scripts
jhudsl
ottrpal:Companion Tools for Open-Source Tools for Training Resources (OTTR)
Tools for converting Open-Source Tools for Training Resources (OTTR) courses into Leanpub or Coursera courses. 'ottrpal' is for use with the OTTR Template repository to create courses.
Maintained by Candace Savonen. Last updated 11 days ago.
3 stars 6.50 score 10 scripts 1 dependents
gisma
uavRmp:UAV Mission Planner
The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI-Litchi supported series or ready to upload control files for the pixhawk-based flight controller as used in the 3DR-Solo or Yuneec series. Additionally it contains some useful tools for digitizing and data manipulation.
Maintained by Chris Reudenbach. Last updated 10 months ago.
cultural-heritagedjidroneflight-planningforest-mappinglitchilow-budget-uavmission-planningphotogrammetrypixhawkpixhawk-controllerqgroundcontrol2litchisolosurveyterrain-followingterrain-mappinguavsyuneec
25 stars 6.48 score 6 scripts
ericmarcon
memoiR:R Markdown and Bookdown Templates to Publish Documents
Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Maintained by Eric Marcon. Last updated 30 days ago.
articlebeamerbookdowngitbooklatextemplatethesis
23 stars 6.44 scorehubverse-org
hubEnsembles:Ensemble Methods for Combining Hub Model Outputs
Functions for combining model outputs (e.g. predictions or estimates) from multiple models into an aggregated ensemble model output.
Maintained by Li Shandross. Last updated 6 months ago.
6 stars 6.43 score 42 scripts 1 dependentsusaid-oha-si
glitr:Adorned SI style plots
Helps create and export ggplot2 charts in the style used by the GH OHA SI team. Includes multiple styles and themes to tweak plots to user needs. Sample testing data also available.
Maintained by Tim Essam. Last updated 3 months ago.
27 stars 6.43 score 279 scripts 1 dependents
mrc-ide
drjacoby:Flexible Markov Chain Monte Carlo via Reparameterization
drjacoby is an R package for performing Bayesian inference via Markov chain monte carlo (MCMC). In addition to being highly flexible it implements some advanced techniques that can improve mixing in tricky situations.
Maintained by Bob Verity. Last updated 9 months ago.
12 stars 6.27 score 77 scriptspik-piam
mrremind:MadRat REMIND Input Data Package
The mrremind packages contains data preprocessing for the REMIND model.
Maintained by Lavinia Baumstark. Last updated 3 days ago.
4 stars 6.25 score 15 scripts 1 dependents
johncoene
packer:An Opinionated Framework for Using 'JavaScript'
Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM', 'yarn', and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' and 'yarn' packages, include 'TypeScript', 'React', or 'Vue' in web applications, and much more.
Maintained by John Coene. Last updated 8 months ago.
148 stars 6.25 score 1 scripts 2 dependentsusaid-oha-si
gophr:Utility functions related to working with the MER Structured Dataset
This packages contains a number of functions for working with the PEPFAR MSD.
Maintained by Aaron Chafetz. Last updated 5 months ago.
1 stars 6.21 score 182 scripts 1 dependents
njlyon0
supportR:Support Functions for Wrangling and Visualization
Suite of helper functions for data wrangling and visualization. The only theme for these functions is that they tend towards simple, short, and narrowly-scoped. These functions are built for tasks that often recur but are not large enough in scope to warrant an ecosystem of interdependent functions.
Maintained by Nicholas J Lyon. Last updated 4 months ago.
5 stars 6.18 score 15 scripts
ohdsi
OmopViewer:Visualise OMOP Results using 'shiny' Applications
Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.
Maintained by Martí Català. Last updated 21 days ago.
3 stars 6.15 score 4 scripts
iheid-library
iheiddown:For Writing Geneva Graduate Institute Documents
A set of tools for writing documents according to Geneva Graduate Institute conventions and regulations. The most common use is for writing and compiling theses or thesis chapters, as drafts or for examination with correct preamble formatting. However, the package also offers users to create HTML presentation slides with 'xaringan', complete problem sets, format posters, and, for course instructors, prepare a syllabus. The package includes additional functions for institutional color palettes, an institutional 'ggplot' theme, a function for counting manuscript words, and a bibliographical analysis toolkit.
Maintained by James Hollway. Last updated 2 years ago.
11 stars 6.14 score 5 scripts
snystrom
cmdfun:Framework for Building Interfaces to Shell Commands
Writing interfaces to command line software is cumbersome. 'cmdfun' provides a framework for building function calls to seamlessly interface with shell commands by allowing lazy evaluation of command line arguments. 'cmdfun' also provides methods for handling user-specific paths to tool installs or secrets like API keys. Its focus is to equally serve package builders who wish to wrap command line software, and to help analysts stay inside R when they might usually leave to execute non-R software.
Maintained by Spencer Nystrom. Last updated 4 years ago.
15 stars 6.13 score 7 scripts 6 dependents
fhdsl
metricminer:Mine Metrics from Common Places on the Web
Mine metrics on common places on the web through the power of their APIs (application programming interfaces). It also helps make the data in a format that is easily used for a dashboard or other purposes. There is an associated dashboard template and tutorials that are underdevelopment that help you fully utilize 'metricminer'.
Maintained by Candace Savonen. Last updated 6 days ago.
2 stars 6.13 score 21 scriptsramikrispin
covid19italy:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.
Maintained by Rami Krispin. Last updated 2 years ago.
47 stars 6.07 score 25 scripts
kforner
srcpkgs:R Source Packages Manager
Manage a collection/library of R source packages. Discover, document, load, test source packages. Enable to use those packages as if they were actually installed. Quickly reload only what is needed on source code change. Run tests and checks in parallel.
Maintained by Karl Forner. Last updated 10 months ago.
11 stars 6.04 score 6 scripts
gabriel-assuncao
PNADcIBGE:Downloading, Reading and Analyzing PNADC Microdata
Provides tools for downloading, reading and analyzing the Continuous National Household Sample Survey - PNADC, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Maintained by Gabriel Assuncao. Last updated 1 years ago.
28 stars 6.02 score 151 scripts 1 dependentsbioc
INDEED:Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.
Maintained by Ressom group. Last updated 5 months ago.
immunooncologysoftwareresearchfieldbiologicalquestionstatisticalmethoddifferentialexpressionmassspectrometrymetabolomics
5 stars 6.02 score 10 scriptsropensci
pkgreviewr:rOpenSci package review project template
Creates files and collects materials necessary to complete an rOpenSci package review. Review files are prepopulated with review package specific metadata. Review package source code is also cloned for local testing and inspection.
Maintained by Maëlle Salmon. Last updated 1 months ago.
reviewropensciropensci-reviewsunconfunconf18
37 stars 5.97 score 28 scriptsbioc
PathoStat:PathoStat Statistical Microbiome Analysis Package
The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
Maintained by Solaiappan Manimaran. Last updated 5 months ago.
microbiomemetagenomicsgraphandnetworkmicroarraypatternlogicprincipalcomponentsequencingsoftwarevisualizationrnaseqimmunooncology
8 stars 5.90 score 8 scripts
simonpcouch
anyflights:Query 'nycflights13'-Like Air Travel Data for Given Years and Airports
Supplies a set of functions to query air travel data for user- specified years and airports. Datasets include on-time flights, airlines, airports, planes, and weather.
Maintained by Simon P. Couch. Last updated 3 months ago.
49 stars 5.90 score 23 scripts
jeffreyrstevens
flashr:Create Flashcards of Terms and Definitions
Provides functions for creating flashcard decks of terms and definitions. This package creates HTML slides using 'revealjs' that can be viewed in the 'RStudio' viewer or a web browser. Users can create flashcards from either existing built-in decks or create their own from CSV files or vectors of function names.
Maintained by Jeffrey R. Stevens. Last updated 1 years ago.
9 stars 5.89 score 171 scriptsropensci
circle:R Client Package for Circle CI
Tools for interacting with the 'Circle CI' API (<https://circleci.com/docs/api/v2/>). Besides executing common tasks such as querying build logs and restarting builds, this package also helps setting up permissions to deploy from builds.
Maintained by Patrick Schratz. Last updated 3 months ago.
api-clientcircle-cicontinuous-deploymentcontinuous-integration
12 stars 5.86 score 3 scripts
hsvab
odbr:Download Data from Brazil's Origin Destination Surveys
Download data from Brazil's Origin Destination Surveys. The package covers both data from household travel surveys, dictionaries of variables, and the spatial geometries of surveys conducted in different years and across various urban areas in Brazil. For some cities, the package will include enhanced versions of the data sets with variables "harmonized" across different years.
Maintained by Haydee Svab. Last updated 2 months ago.
16 stars 5.85 score 11 scripts
quexiang
OpenMindat:Quickly Retrieve Datasets from the 'Mindat' API
The goal of OpenMindat R package is to provide functions for users or machines to quickly and easily retrieve datasets from the mindat.org API (<https://api.mindat.org/schema/redoc/>).
Maintained by Xiang Que. Last updated 2 months ago.
34 stars 5.83 score 3 scripts
jimbrig
lossrx:Actuarial Loss Development and Reserving with R
Actuarial Loss Development and Reserving Helper Functions and ShinyApp.
Maintained by Jimmy Briggs. Last updated 3 months ago.
actuarial-scienceclaims-dataclaims-reservingdata-scienceinsurancemodellingproperty-casualtyreservingrshinyworkflow
14 stars 5.82 score 7 scripts
modeloriented
modelDown:Make Static HTML Website for Predictive Models
Website generator with HTML summaries for predictive models. This package uses 'DALEX' explainers to describe global model behavior. We can see how well models behave (tabs: Model Performance, Auditor), how much each variable contributes to predictions (tabs: Variable Response) and which variables are the most important for a given model (tabs: Variable Importance). We can also compare Concept Drift for pairs of models (tabs: Drifter). Additionally, data available on the website can be easily recreated in current R session. Work on this package was financially supported by the NCN Opus grant 2017/27/B/ST6/01307 at Warsaw University of Technology, Faculty of Mathematics and Information Science.
Maintained by Kamil Romaszko. Last updated 4 years ago.
121 stars 5.80 score 15 scriptsbioc
MetID:Network-based prioritization of putative metabolite IDs
This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.
Maintained by Zhenzhi Li. Last updated 5 months ago.
assaydomainbiologicalquestioninfrastructureresearchfieldstatisticalmethodtechnologyworkflowstepnetworkkegg
1 stars 5.74 score 110 scripts
wa-department-of-agriculture
soils:Visualize and Report Soil Health Data
Collection of soil health data visualization and reporting tools, including a RStudio project template with everything you need to generate custom HTML and Microsoft Word reports for each participant in your soil health sampling project.
Maintained by Jadey N Ryan. Last updated 6 days ago.
10 stars 5.73 score 9 scriptsbeanumber
macleish:Retrieve Data from MacLeish Field Station
Download data from the Ada and Archibald MacLeish Field Station in Whately, MA. The Ada and Archibald MacLeish Field Station is a 260-acre patchwork of forest and farmland located in West Whately, MA that provides opportunities for faculty and students to pursue environmental research, outdoor education, and low-impact recreation (see <https://www.smith.edu/about-smith/sustainable-smith/macleish> for more information). This package contains weather data over several years, and spatial data on various man-made and natural structures.
Maintained by Benjamin S. Baumer. Last updated 3 years ago.
2 stars 5.72 score 87 scripts
maraab23
ggseqplot:Render Sequence Plots using 'ggplot2'
A set of wrapper functions that mainly re-produces most of the sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base R to produce the plots this library draws on 'ggplot2'. The plots are produced on the basis of a sequence object defined with TraMineR::seqdef(). The package automates the reshaping and plotting of sequence data. Resulting plots are of class 'ggplot', i.e. components can be added and tweaked using '+' and regular 'ggplot2' functions.
Maintained by Marcel Raab. Last updated 4 months ago.
ggplot2sequence-analysistraminervisualization
14 stars 5.70 score 18 scripts
tiago-simoes
EvoPhylo:Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Maintained by Tiago Simoes. Last updated 2 years ago.
4 stars 5.66 score 19 scriptshubverse-org
hubData:Tools for accessing and working with hubverse data
A set of utility functions for accessing and working with forecast and target data from Infectious Disease Modeling Hubs.
Maintained by Anna Krystalli. Last updated 4 months ago.
3 stars 5.66 score 60 scripts 2 dependentsmazamascience
MazamaLocationUtils:Manage Spatial Metadata for Known Locations
Utility functions for discovering and managing metadata associated with spatially unique "known locations". Applications include all fields of environmental monitoring (e.g. air and water quality) where data are collected at stationary sites.
Maintained by Jonathan Callahan. Last updated 4 months ago.
5.64 score 108 scriptscorrelaid
pocketapi:Wrapper Around the 'Pocket' API
Functions that interface with the 'Pocket' API (<https://getpocket.com/developer/>). Allows the user to get, add, and modify items in their own 'Pocket' account.
Maintained by Frie Preu. Last updated 4 years ago.
17 stars 5.63 score 5 scripts
eogrady21
vprr:Processing and Visualization of Video Plankton Recorder Data
An oceanographic data processing package for analyzing and visualizing Video Plankton Recorder data. This package was developed at 'Bedford Institute of Oceanography'. Functions are designed to process automated image classification output and create organized and easily portable data products.
Maintained by Emily OGrady. Last updated 2 months ago.
2 stars 5.61 score 17 scripts
nflverse
nflversedata:nflverse data storage functions
This repository holds automated data releases for nflverse projects and helper functions for managing the uploads.
Maintained by Tan Ho. Last updated 1 months ago.
221 stars 5.57 score
dnme-minturdep
comunicacion:DNMyE - Comunicación
Herramientas para la comunicación de la Dirección Nacional de Mercados y Estadística de la Subsecretaría de Turismo de Argentina.
Maintained by Juan Pablo Ruiz Nicolini. Last updated 8 months ago.
4 stars 5.57 score 124 scripts 1 dependents
bioc
chevreulPlot:Plots used in the chevreulPlot package
Tools for plotting SingleCellExperiment objects in the chevreulPlot package. Includes functions for analysis and visualization of single-cell data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 1 months ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
5.56 score 2 scripts 1 dependentsbioc
methylclock:Methylclock - DNA methylation-based clocks
This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.
Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.
dnamethylationbiologicalquestionpreprocessingstatisticalmethodnormalizationcpp
39 stars 5.52 score 28 scriptsusaid-oha-si
mindthegap:Mind the Gap
Package to tidy UNAIDS estimates (from the EDMS database) as well as plot trends in UNAIDS 95 goals and ART coverage gap by country.
Maintained by Karishma Srikanth. Last updated 3 months ago.
5 stars 5.51 score 13 scriptsropensci
mcbette:Model Comparison Using 'babette'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).
Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.
7 stars 5.50 score 18 scriptsbioc
MotifPeeker:Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
MotifPeeker is used to compare and analyse datasets from epigenomic profiling methods with motif enrichment as the key benchmark. The package outputs an HTML report consisting of three sections: (1. General Metrics) Overview of peaks-related general metrics for the datasets (FRiP scores, peak widths and motif-summit distances). (2. Known Motif Enrichment Analysis) Statistics for the frequency of user-provided motifs enriched in the datasets. (3. De-Novo Motif Enrichment Analysis) Statistics for the frequency of de-novo discovered motifs enriched in the datasets and compared with known motifs.
Maintained by Hiranyamaya Dash. Last updated 3 months ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsmotifdiscoverysequencematchingsoftwarealignmentbioconductorbioconductor-packagechip-seqepigenomicsinteractive-reportmotif-enrichment-analysis
2 stars 5.48 score 6 scriptsropensci
grainchanger:Moving-Window and Direct Data Aggregation
Data aggregation via moving window or direct methods. Aggregate a fine-resolution raster to a grid. The moving window method smooths the surface using a specified function within a moving window of a specified size and shape prior to aggregation. The direct method simply aggregates to the grid using the specified function.
Maintained by Laura Graham. Last updated 2 years ago.
52 stars 5.46 score 28 scripts
jonthegeek
beekeeper:Rapidly Scaffold API Client Packages
Automatically generate R package skeletons from 'application programming interfaces (APIs)' that follow the 'OpenAPI Specification (OAS)'. The skeletons implement best practices to streamline package development.
Maintained by Jon Harmon. Last updated 6 months ago.
53 stars 5.42 score 2 scriptsthinkr-open
lozen:Management tools for missions
Management tools for missions (internal and external). Includes weekly, GL projects, etc.
Maintained by Sébastien Rochette. Last updated 12 months ago.
7 stars 5.42 score 14 scripts
simon-smart88
shinyscholar:A Template for Creating Reproducible 'shiny' Applications
Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.
Maintained by Simon E. H. Smart. Last updated 7 days ago.
22 stars 5.40 score 5 scripts
jbryer
brickset:Interface with the Brickset API for Getting Data About LEGO Sets
Interface with the 'Brickset' API <https://brickset.com/article/52664/api-version-3-documentation> for getting data about LEGO sets. Data sets that can be used for teaching and learning without the need of a 'Brickset' account and API key are also included. Includes all LEGO since through the end of 2023.
Maintained by Jason Bryer. Last updated 1 months ago.
14 stars 5.40 score 12 scripts
maelstrom-research
madshapR:Support Technical Processes Following 'Maelstrom Research' Standards
Functions to support rigorous processes in data cleaning, evaluation, and documentation across datasets from different studies based on Maelstrom Research guidelines. The package includes the core functions to evaluate and format the main inputs that define the process, diagnose errors, and summarize and evaluate datasets and their associated data dictionaries. The main outputs are clean datasets and associated metadata, and tabular and visual summary reports. As described in Maelstrom Research guidelines for rigorous retrospective data harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Maintained by Guillaume Fabre. Last updated 11 months ago.
2 stars 5.40 score 28 scripts 3 dependentssportsdataverse
wehoop:Access Women's Basketball Play by Play Data
A utility for working with women's basketball data. A scraping and aggregating interface for the WNBA Stats API <https://stats.wnba.com/> and ESPN's <https://www.espn.com> women's college basketball and WNBA statistics. It provides users with the capability to access the game play-by-plays, box scores, standings and results to analyze the data for themselves.
Maintained by Saiem Gilani. Last updated 8 months ago.
college-basketballespnespn-statsncaancaa-basketballprofessional-basketball-datasportsdataversewnbawnba-playerswnba-statswomens-basketball
31 stars 5.40 score 54 scriptsbioc
chevreulProcess:Tools for managing SingleCellExperiment objects as projects
Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 2 months ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
5.38 score 2 scripts 2 dependents
insightsengineering
verdepcheck:Check Package using Various Versions of Dependencies
Derive package dependencies from DESCRIPTION file using various strategies and run "R CMD CHECK" to validate package compatibility.
Maintained by Pawel Rucki. Last updated 6 months ago.
7 stars 5.36 score 1 scriptsmazamascience
MazamaTimeSeries:Core Functionality for Environmental Time Series
Utility functions for working with environmental time series data from known locations. The compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Ephemerides calculations are based on code originally found in NOAA's "Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.
Maintained by Jonathan Callahan. Last updated 1 years ago.
5.27 score 62 scripts 1 dependents
harrison4192
validata:Validate Data Frames
Functions for validating the structure and properties of data frames. Answers essential questions about a data set after initial import or modification. What are the unique or missing values? What columns form a primary key? What are the properties of the numeric or categorical columns? What kind of overlap or mapping exists between 2 columns?
Maintained by Harrison Tietze. Last updated 27 days ago.
6 stars 5.26 score 4 scripts 1 dependents
nceas
scicomptools:Tools Developed by the NCEAS Scientific Computing Support Team
Set of tools to import, summarize, wrangle, and visualize data. These functions were originally written based on the needs of the various synthesis working groups that were supported by the National Center for Ecological Analysis and Synthesis (NCEAS). These tools are meant to be useful inside and outside of the context for which they were designed.
Maintained by Angel Chen. Last updated 5 months ago.
9 stars 5.26 score 6 scriptsropensci
roreviewapi:Plumber API to report package structure and function
Plumber API to report package structure and function.
Maintained by Mark Padgham. Last updated 1 months ago.
4 stars 5.26 score
coneill-math
m2r:Interface to 'Macaulay2'
Persistent interface to 'Macaulay2' <http://www.math.uiuc.edu/Macaulay2/> and front-end tools facilitating its use in the 'R' ecosystem. For details see Kahle et. al. (2020) <doi:10.18637/jss.v093.i09>.
Maintained by David Kahle. Last updated 5 years ago.
5 stars 5.23 score 34 scripts
usaid-mozambique
sismar:Arrumar dados SISMA
Fornece um conjunto de funções para a criação de conjuntos de dados analíticos a partir de downloads do SISMA e DISA. Inclui funções que arrumam os ficheiros para um formato longo, removem variáveis desnecessárias, e criam colunas úteis para a análise.
Maintained by Joe Lara. Last updated 4 days ago.
2 stars 5.23 score 9 scripts
openbiox
contribution:A Tiny Contribution Table Generator Based on 'ggplot2'
Contribution table for credit assignment based on 'ggplot2'. This can improve the author contribution information in academic journals and personal CV.
Maintained by Shixiang Wang. Last updated 2 years ago.
contributioncreditggplot2research
11 stars 5.20 score 29 scriptspik-piam
modelstats:Run Analysis Tools
A collection of tools to analyze model runs.
Maintained by Anastasis Giannousakis. Last updated 14 days ago.
1 stars 5.19 score 2 scriptsbioc
HubPub:Utilities to create and use Bioconductor Hubs
HubPub provides users with functionality to help with the Bioconductor Hub structures. The package provides the ability to create a skeleton of a Hub style package that the user can then populate with the necessary information. There are also functions to help add resources to the Hub package metadata files as well as publish data to the Bioconductor S3 bucket.
Maintained by Kayla Interdonato. Last updated 17 days ago.
dataimportinfrastructuresoftwarethirdpartyclientbioconductor-package
3 stars 5.18 score 4 scriptsropengov
rogtemplate:'pkgdown' Template for 'rOpenGov' Packages
This is a private template for use by core rOpenGov packages. Please don’t use for your own code.
Maintained by Diego Hernangómez. Last updated 13 days ago.
ropengovtemplategithub-actionspkgdownpkgdown-template
2 stars 5.16 score 3 scriptsramikrispin
covid19sf:The Covid19 San Francisco Dataset
Provides a verity of summary tables of the Covid19 cases in San Francisco. Data source: San Francisco, Department of Public Health - Population Health Division <https://datasf.org/opendata/>.
Maintained by Rami Krispin. Last updated 2 years ago.
12 stars 5.16 score 12 scripts
baumer-lab
fec16:Data Package for the 2016 United States Federal Elections
Easily analyze relational data from the United States 2016 federal election cycle as reported by the Federal Election Commission. This package contains data about candidates, committees, and a variety of different financial expenditures. Data is from <https://www.fec.gov/data/browse-data/?tab=bulk-data>.
Maintained by Marium Tapal. Last updated 2 years ago.
2 stars 5.15 score 47 scripts
larsenlab
hlaR:Tools for HLA Data
A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.
Maintained by Joan Zhang. Last updated 2 years ago.
7 stars 5.15 score 9 scripts
miriamesteve
GSSTDA:Progression Analysis of Disease with Survival using Topological Data Analysis
Mapper-based survival analysis with transcriptomics data is designed to carry out. Mapper-based survival analysis is a modification of Progression Analysis of Disease (PAD) where survival data is taken into account in the filtering function. More details in: J. Fores-Martos, B. Suay-Garcia, R. Bosch-Romeu, M.C. Sanfeliu-Alonso, A. Falco, J. Climent, "Progression Analysis of Disease with Survival (PAD-S) by SurvMap identifies different prognostic subgroups of breast cancer in a large combined set of transcriptomics and methylation studies" <doi:10.1101/2022.09.08.507080>.
Maintained by Miriam Esteve. Last updated 8 months ago.
2 stars 5.15 score 7 scripts
guifabre
fabR:Wrapper Functions Collection Used in Data Pipelines
The goal of this package is to provide wrapper functions in the data cleaning and cleansing processes. These function helps in messages and interaction with the user, keep track of information in pipelines, help in the wrangling, munging, assessment and visualization of data frame-like material.
Maintained by Guillaume Fabre. Last updated 11 months ago.
1 stars 5.14 score 23 scripts 4 dependentsusaid-oha-si
grabr:OHA/SI APIs Package
Provides a series of base functions useful to the GH OHA SI team. These function extend the utility functions in glamr, focusing primarily on API utility functions.
Maintained by Aaron Chafetz. Last updated 6 months ago.
1 stars 5.14 score 69 scripts
s-fleck
testthis:Utils and 'RStudio' Addins to Make Testing Even More Fun
Utility functions and 'RStudio' addins for writing, running and organizing automated tests. Integrates tightly with the packages 'testthat', 'devtools' and 'usethis'. Hotkeys can be assigned to the 'RStudio' addins for running tests in a single file or to switch between a source file and the associated test file. In addition, testthis provides function to manage and run tests in subdirectories of the test/testthat directory.
Maintained by Stefan Fleck. Last updated 3 years ago.
rstudiorstudio-addinrstudio-addinstestingtestthat
33 stars 5.12 score 20 scriptspik-piam
piamPlotComparison:Create comparison plots for your model results
A frameworks to create comparison plots for your model results.
Maintained by Falk Benke. Last updated 3 months ago.
5.12 score 11 scripts 8 dependentsbioc
chevreulShiny:Tools for managing SingleCellExperiment objects as projects
Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.
Maintained by Kevin Stachelek. Last updated 28 days ago.
coveragernaseqsequencingvisualizationgeneexpressiontranscriptionsinglecelltranscriptomicsnormalizationpreprocessingqualitycontroldimensionreductiondataimport
5.08 score
csids
plnr:A Framework for Planning and Executing Analyses
A comprehensive framework for planning and executing analyses in R. It provides a structured approach to running the same function multiple times with different arguments, executing multiple functions on the same datasets, and creating systematic analyses across multiple strata or variables. The framework is particularly useful for applying the same analysis across multiple strata (e.g., locations, age groups), running statistical methods on multiple variables (e.g., exposures, outcomes), generating multiple tables or graphs for reports, and creating systematic surveillance analyses. Key features include efficient data management, structured analysis planning, flexible execution options, built-in debugging tools, and hash-based caching.
Maintained by Richard Aubrey White. Last updated 12 days ago.
3 stars 5.08 score 1 scripts
yanrong-stacy-song
creditr:Credit Default Swaps
Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.
Maintained by Yanrong Song. Last updated 8 days ago.
5.05 score 32 scripts
seewooli
IRTest:Parameter Estimation of Item Response Theory with Estimation of Latent Distribution
Item response theory (IRT) parameter estimation using marginal maximum likelihood and expectation-maximization algorithm (Bock & Aitkin, 1981 <doi:10.1007/BF02293801>). Within parameter estimation algorithm, several methods for latent distribution estimation are available. Reflecting some features of the true latent distribution, these latent distribution estimation methods can possibly enhance the estimation accuracy and free the normality assumption on the latent distribution.
Maintained by Seewoo Li. Last updated 1 months ago.
2 stars 5.04 score 8 scripts
dieghernan
pkgdev:Helpers to Develop a Package using GitHub Actions
A small set of functions that takes advantage of GitHub Actions for making your life easier as a R package developer. This package is primarily intended for personal use, however feel free to use it (at your own risk :)).
Maintained by Diego Hernangómez. Last updated 7 days ago.
developer-toolsexperimentalgithub-actions
4 stars 5.00 score 7 scripts
alphaprime7
normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Maintained by Tingwei Adeck. Last updated 5 months ago.
1 stars 4.98 score 12 scripts
openwashdata
washr:Publication Toolkit for Water, Sanitation and Hygiene (WASH) Data
A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.
Maintained by Colin Walder. Last updated 5 months ago.
2 stars 4.95 score 7 scripts
ropenspain
rostemplate:Plantilla 'pkgdown' para los paquetes de 'rOpenSpain'
Plantilla privada para uso exclusivo de los paquetes de rOpenSpain.
Maintained by Diego Hernangómez. Last updated 13 days ago.
github-actionspkgdownropenspaintemplateyaml
3 stars 4.95 score 3 scripts
qile0317
FastUtils:Fast, Readable Utility Functions
A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible. Exported names are designed to be readable, with longer names possessing short aliases.
Maintained by Qile Yang. Last updated 4 months ago.
scientific-computingutilitiesutilitycpp
2 stars 4.95 score 2 scripts
ryan-riggs
RivRetrieve:Retrieve Global River Gauge Data
Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.
Maintained by Ryan Riggs. Last updated 3 months ago.
9 stars 4.95 score 7 scripts
nhs-r-community
NHSRpopulation:Indices of Multiple Deprivation (IMD) for England
This package includes functions to retrieve the Indices of Multiple Deprivation (IMD) data from the ONS by LSOA, currently for England.
Maintained by Zoë Turner. Last updated 10 months ago.
11 stars 4.94 score 5 scripts
mlysy
rdoxygen:Create Doxygen Documentation for Source Code
Create 'doxygen' documentation for source code in R packages, and optionally make it accessible as an R vignette. Includes a 'RStudio' Addin to easily trigger the doxygenize process.
Maintained by Clemens Schmid. Last updated 6 years ago.
17 stars 4.93 score 6 scripts
vnijs
gitgadget:'Rstudio' Addin for Version Control and Assignment Management using Git
An 'Rstudio' addin for version control that allows users to clone repositories, create and delete branches, and sync forks on GitHub, GitLab, etc. Furthermore, the addin uses the GitLab API to allow instructors to create forks and merge requests for all students/teams with one click of a button.
Maintained by Vincent Nijs. Last updated 2 years ago.
17 stars 4.93 score 2 scripts
vincentguyader
shiny2docker:Generate Dockerfiles for 'Shiny' Applications
Automates the creation of Dockerfiles for deploying 'Shiny' applications. By integrating with 'renv' for dependency management and leveraging Docker-based solutions, it simplifies the process of containerizing 'Shiny' apps, ensuring reproducibility and consistency across different environments. Additionally, it facilitates the setup of CI/CD pipelines for building Docker images on both GitLab and GitHub.
Maintained by Vincent Guyader. Last updated 2 months ago.
8 stars 4.90 score
netique
buildr:Organize & Run Build Scripts Comfortably
Working with reproducible reports or any other similar projects often require to run the script that builds the output file in a specified way. 'buildr' can help you organize, modify and comfortably run those scripts. The package provides a set of functions that interactively guides you through the process and that are available as 'RStudio' Addin, meaning you can set up the keyboard shortcuts, enabling you to choose and run the desired build script with one keystroke anywhere anytime.
Maintained by Jan Netik. Last updated 12 months ago.
addinbuildrkeyboard-shortcutrstudio-addin
15 stars 4.88 score 8 scriptsmazamascience
MazamaSpatialPlots:Thematic Plots for Mazama Spatial Datasets
A suite of convenience functions for generating US state and county thematic maps using datasets from the MazamaSpatialUtils package.
Maintained by Jonathan Callahan. Last updated 2 months ago.
4.84 score 23 scripts
scholaempirica
reschola:The Schola Empirica Package
A collection of utilies, themes and templates for data analysis at Schola Empirica.
Maintained by Jan Netík. Last updated 6 months ago.
4 stars 4.83 score 14 scripts
mkearney
pkgverse:Build a Meta-Package Universe
Build your own universe of packages similar to the 'tidyverse' package <https://tidyverse.org/> with this meta-package creator. Create a package-verse, or meta package, by supplying a custom name for the collection of packages and the vector of desired package names to include– and optionally supply a destination directory, an indicator of whether to keep the created package directory, and/or a vector of verbs implement via the 'usethis' <http://usethis.r-lib.org/> package.
Maintained by Michael Wayne Kearney. Last updated 6 years ago.
121 stars 4.78 score 6 scripts
seewe
dataCompare:A 'shiny' App to Compare Two Data Frames
A tool developed with the 'Golem' framework which provides an easier way to check cells differences between two data frames. The user provides two data frames for comparison, selects IDs variables identifying each row of input data, then clicks a button to perform the comparison. Several 'R' package functions are used to describe the data and perform the comparison in the server of the application. The main ones are comparedf() from 'arsenal' and skim() from 'skimr'. For more details see the description of comparedf() from the 'arsenal' package and that of skim() from the 'skimr' package.
Maintained by Sergio Ewane Ebouele. Last updated 3 months ago.
2 stars 4.78 score 4 scripts
lter
ltertools:Tools Developed by the Long Term Ecological Research Community
Set of the data science tools created by various members of the Long Term Ecological Research (LTER) community. These functions were initially written largely as standalone operations and have later been aggregated into this package.
Maintained by Nicholas Lyon. Last updated 4 days ago.
3 stars 4.78 score 4 scriptsharrison4192
tidybins:Make Tidy Bins
Multiple ways to bin numeric columns with a tidy output. Wraps a variety of existing binning methods into one function, and includes a new method for binning by equal value, which is useful for sales data. Provides a function to automatically summarize the properties of the binned columns.
Maintained by Harrison Tietze. Last updated 10 months ago.
4 stars 4.78 score 2 scripts 1 dependents
aberhrml
metaboData:Example Metabolomics Data Sets
Data sets from a variety of biological sample matrices, analysed using a number of mass spectrometry based metabolomic analytical techniques. The example data sets are stored remotely using GitHub releases <https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package. The package also includes the 'abr1' FIE-MS data set from the 'FIEmspro' package <https://users.aber.ac.uk/jhd/> <doi:10.1038/nprot.2007.511>.
Maintained by Jasen Finch. Last updated 3 years ago.
datadatasetsfie-hrmsfie-msmass-spectrometrymetabolomics
1 stars 4.72 score 104 scripts
jancaha
CzechData:Download various datasets (including spatial data) for the Czech Republic
Download various datasets (including spatial data) for the Czech Republic.
Maintained by Jan Caha. Last updated 2 years ago.
7 stars 4.70 score 16 scripts 1 dependents
pakillo
template:Generic template for data analysis projects structured as R packages
This package works as a template for new research or data analysis projects, under the idea of having everything (data, R scripts, functions and manuscript/reports) contained in the same package (a 'research compendium') to facilitate collaboration and promote reproducibility.
Maintained by Francisco Rodriguez-Sanchez. Last updated 4 years ago.
project-templateresearch-compendiumworkflow
175 stars 4.70 score 57 scriptshubverse-org
hubValidations:Testing framework for hubverse hub validations
This package aims at providing a simple interface to run validations on data and metadata submitted to a hubverse modeling hub. Validation tests can be run at different levels (single file, single folder, whole repository) and locally as well as part of a continuous integration workflow.
Maintained by Anna Krystalli. Last updated 19 days ago.
1 stars 4.67 score 27 scripts 1 dependents
mrchypark
sendgridr:Mail Sender Using 'Sendgrid' Service
Send email using 'Sendgrid' <https://sendgrid.com/en-us> mail API(v3) <https://docs.sendgrid.com/api-reference/how-to-use-the-sendgrid-v3-api/authentication>.
Maintained by Chanyub Park. Last updated 1 years ago.
hacktoberfesthacktoberfest2021mailmailersendgrid
23 stars 4.66 score 10 scriptsbioc
methodical:Discovering genomic regions where methylation is strongly associated with transcriptional activity
DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.
Maintained by Richard Heery. Last updated 2 months ago.
dnamethylationmethylationarraytranscriptiongenomewideassociationsoftwareopenjdk
4.65 score 14 scriptsgabriel-assuncao
PNSIBGE:Downloading, Reading and Analyzing PNS Microdata
Provides tools for downloading, reading and analyzing the National Survey of Health - PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Maintained by Gabriel Assuncao. Last updated 1 years ago.
12 stars 4.64 score 24 scripts 1 dependents
techtonique
ahead:Time Series Forecasting with uncertainty quantification
Univariate and multivariate time series forecasting with uncertainty quantification.
Maintained by T. Moudiki. Last updated 1 months ago.
forecastingmachine-learningpredictive-modelingstatistical-learningtime-seriestime-series-forecastinguncertainty-quantificationcpp
21 stars 4.63 score 51 scriptspik-piam
limes:The liMES R package
Contains the LIMES-specific routines for data and model output manipulation.
Maintained by Sebastian Osorio. Last updated 14 days ago.
1 stars 4.63 score 5 scriptsmrchypark
multilinguer:Gentle Language Installer for R User
Provides install functions of other languages such as 'java', 'python'.
Maintained by Chanyub Park. Last updated 3 years ago.
hacktoberfesthacktoberfest2021
7 stars 4.63 score 121 scriptshubverse-org
hubEvals:Basic tools for scoring hubverse forecasts
Using functionality from the scoringutils package, this software provides basic tools for scoring hubverse forecasts.
Maintained by Nicholas Reich. Last updated 3 days ago.
4 stars 4.62 score 8 scripts 1 dependents
maple-health-group
easysurv:Simplify Survival Data Analysis and Model Fitting
Inspect survival data, plot Kaplan-Meier curves, assess the proportional hazards assumption, fit parametric survival models, predict and plot survival and hazards, and export the outputs to 'Excel'. A simple interface for fitting survival models using flexsurv::flexsurvreg(), flexsurv::flexsurvspline(), flexsurvcure::flexsurvcure(), and survival::survreg().
Maintained by Niall Davison. Last updated 9 months ago.
4 stars 4.60 score 7 scripts
skvrnami
hlidacr:Access Data from the 'Hlídač Státu' API
Provides access to datasets published by 'Hlídač státu' <https://www.hlidacstatu.cz/>, a Czech watchdog, via their API.
Maintained by Michael Škvrňák. Last updated 4 years ago.
czech-republicdatasetsopen-data
8 stars 4.60 score 6 scriptspik-piam
reporttransport:Reporting package for edgeTransport
This package contains edgeTransport-specific routines to report model results. The main functionality is to generate transport reporting variables in MIF format from a given edgeTransport model run folder or REMIND input data.
Maintained by Johanna Hoppe. Last updated 2 months ago.
4.60 score 9 scripts 3 dependents
giocomai
castarter:Content Analysis Starter Toolkit
Consistent approaches for basic web scraping, text mining and word frequency analysis of textual datasets.
Maintained by Giorgio Comai. Last updated 17 hours ago.
3 stars 4.59 score 2 scripts
pharmaverse
envsetup:Support the Setup of the R Environment for Clinical Trial Programming Workflows
The purpose of this package is to support the setup the R environment. The two main features are 'autos', to automatically source files and/or directories into your environment, and 'paths' to consistently set path objects across projects for input and output. Both are implemented using a configuration file to allow easy, custom configurations that can be used for multiple or all projects.
Maintained by Nicholas Masel. Last updated 10 months ago.
7 stars 4.54 score 5 scriptsropensci
repometrics:Metrics for Your Code Repository
Metrics for your code repository. Call one function to generate an interactive dashboard displaying the state of your code.
Maintained by Mark Padgham. Last updated 19 days ago.
2 stars 4.53 score
fairdatapipeline
rDataPipeline:Functions to Interact with the 'FAIR Data Pipeline'
R implementation of the 'FAIR Data Pipeline API'. The 'FAIR Data Pipeline' is intended to enable tracking of provenance of FAIR (findable, accessible and interoperable) data used in epidemiological modelling.
Maintained by Ryan Field. Last updated 4 months ago.
4 stars 4.52 score 11 scriptsinbo
INBOmd:Markdown Templates for INBO
Several templates to generate reports, presentations and posters.
Maintained by Thierry Onkelinx. Last updated 1 years ago.
12 stars 4.52 score 11 scriptspik-piam
piamValidation:Validation Tools for PIK-PIAM
The piamValidation package provides validation tools for the Potsdam Integrated Assessment Modelling environment.
Maintained by Pascal Weigmann. Last updated 4 days ago.
1 stars 4.49 score 13 scriptsr-lib
ghapps:Authenticate as a 'GitHub' App
'GitHub' apps provide a powerful way to manage fine grained programmatic access to specific 'git' repositories, without having to create dummy users, and which are safer than a personal access token for automated tasks. This package extends the 'gh' package to let you authenticate and interact with 'GitHub' <https://docs.github.com/en/rest/overview> in 'R' as an app.
Maintained by Jeroen Ooms. Last updated 6 months ago.
20 stars 4.48 score 1 scriptsbioc
BiocBook:Write, containerize, publish and version Quarto books with Bioconductor
A BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).
Maintained by Jacques Serizay. Last updated 5 months ago.
infrastructurereportwritingsoftware
3 stars 4.48 score 4 scriptsdnme-minturdep
herramientas:Conjunto de funciones para el procesamiento de datos en la DNMyE
Caja de herramientas para el procesamiento de datos en la Dirección Nacional de Mercados y Estadísticas del Ministerio de Turismo y Deportes de la Nación.
Maintained by Juan Juara. Last updated 1 years ago.
5 stars 4.47 score 79 scripts 1 dependentshubverse-org
hubVis:Plotting methods for hub models output
Plotting methods for hub models output.
Maintained by Lucie Contamin. Last updated 4 months ago.
3 stars 4.44 score 22 scripts 1 dependentshubverse-org
hubDevs:Utilities for Creating and Standardising Hubverse Packages
What the package does (one paragraph).
Maintained by Anna Krystalli. Last updated 3 months ago.
4.43 score 3 scripts
milesmcbain
tflow:Setup a project in the tflow style for using the targets package
Has a function that sets up an R workflow in the dflow style, using targets.
Maintained by Miles McBain. Last updated 9 months ago.
93 stars 4.41 score 11 scripts
setempler
miscset:Miscellaneous Tools Set
A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.
Maintained by Sven E. Templer. Last updated 8 years ago.
1 stars 4.40 score 50 scripts
chi2labs
moodleR:Helper Functions to Work with 'Moodle' Data
A collection of functions to connect to a 'Moodle' database, cache relevant tables locally and generate learning analytics. 'Moodle' is an open source Learning Management System (LMS) developed by MoodleHQ. For more information about Moodle, visit <https://moodle.org>.
Maintained by Aleksander Dietrichson. Last updated 3 years ago.
learning-analyticsmoodlemoodle-data
5 stars 4.40 score 9 scripts
annechao
MF.beta4:Measuring Ecosystem Multi-Functionality and Its Decomposition
Provide simple functions to (i) compute a class of multi-functionality measures for a single ecosystem for given function weights, (ii) decompose gamma multi-functionality for pairs of ecosystems and K ecosystems (K can be greater than 2) into a within-ecosystem component (alpha multi-functionality) and an among-ecosystem component (beta multi-functionality). In each case, the correlation between functions can be corrected for. Based on biodiversity and ecosystem function data, this software also facilitates graphics for assessing biodiversity-ecosystem functioning relationships across scales.
Maintained by Anne Chao. Last updated 4 months ago.
4.40 score 3 scripts
michbur
AmpGram:Prediction of Antimicrobial Peptides
Predicts antimicrobial peptides using random forests trained on the n-gram encoded peptides (10.3390/ijms21124310). The implemented algorithm can be accessed from both the command line and shiny-based GUI. The AmpGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/michbur/AmpGramModel>.
Maintained by Michal Burdukiewicz. Last updated 3 years ago.
4 stars 4.38 score 5 scriptshelske
changer:Change R Package Name
Changing the name of an existing R package is annoying but common task especially in the early stages of package development. This package (mostly) automates this task.
Maintained by Jouni Helske. Last updated 3 years ago.
47 stars 4.37 score 2 scripts
rmi-pacta
pacta.data.preparation:Prepare Data for PACTA for Investors
This package provides tools to prepare input datasets to be run in the PACTA_analysis tool.
Maintained by CJ Yetman. Last updated 5 months ago.
climate-changepactapactaversesustainable-finance
1 stars 4.36 score 11 scripts 1 dependentsthinkr-open
papillon:Build And Highlight Package Documentation With Customized Templates
Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.
Maintained by Sébastien Rochette. Last updated 2 years ago.
11 stars 4.34 score 4 scripts
bioc
oppti:Outlier Protein and Phosphosite Target Identifier
The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.
Maintained by Abdulkadir Elmas. Last updated 5 months ago.
proteomicsregressiondifferentialexpressionbiomedicalinformaticsgenetargetgeneexpressionnetwork
2 stars 4.30 score 2 scriptsbioc
BiocWorkflowTools:Tools to aid the development of Bioconductor Workflow packages
Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.
Maintained by Mike Smith. Last updated 5 months ago.
4.30 score 10 scripts
hugofitipaldi
covidsymptom:COVID Symptom Study Sweden Open Dataset
The COVID Symptom Study is a non-commercial project that uses a free mobile app to facilitate real-time data collection of symptoms, exposures, and risk factors related to COVID19. The package allows easy access to summary statistics data from COVID Symptom Study Sweden.
Maintained by Hugo Fitipaldi. Last updated 11 months ago.
4 stars 4.30 score 7 scripts
green-striped-gecko
dartRverse:Install and Load the 'dartRverse' Suits of Packages
Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.
Maintained by Bernd Gruber. Last updated 18 days ago.
2 stars 4.27 score 47 scriptsfhdsl
githubr:Easier to Use API Wrapper for 'GitHub'
This is a 'GitHub' API wrapper for R. <https://docs.github.com/en/rest> It uses the 'gh' package but has things wrapped up for convenient use cases.
Maintained by Candace Savonen. Last updated 1 years ago.
1 stars 4.27 score 370 scripts
conig
revise:Dynamic Revision Letters for 'Rmarkdown' Manuscripts
Extracts tagged text from markdown manuscripts for inclusion in dynamically generated revision letters. Provides an R markdown template based on papaja::revision_letter_pdf() with comment cross-referencing, a system for managing multiple sections of extracted text, and a way to automatically determine the page number of quoted sections from PDF manuscripts.
Maintained by James Conigrave. Last updated 28 days ago.
3 stars 4.26 score