R-universe search: needs:credentials

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

r-lib

usethis:Automate Package and Project Setup

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

Maintained by Jennifer Bryan. Last updated 24 days ago.

github setup

869 stars 17.54 score 5.6k scripts 336 dependents

ropensci

gert:Simple Git Client for R

Simple git client for R based on 'libgit2' <https://libgit2.org> with support for SSH and HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors and data-frames) for their arguments and return values. User credentials are shared with command line 'git' through the git-credential store and ssh keys stored on disk or ssh-agent.

Maintained by Jeroen Ooms. Last updated 4 days ago.

libgit2

154 stars 14.85 score 158 scripts 367 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 22 days ago.

359 stars 11.33 score 191 scripts 1 dependents

ropensci

ssh:Secure Shell (SSH) Client for R

Connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client.

Maintained by Jeroen Ooms. Last updated 3 days ago.

libssh ssh ssh-client

129 stars 11.33 score 128 scripts 10 dependents

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.

analytics api google googleanalyticsr googleauthr

262 stars 10.11 score 680 scripts 1 dependents

r-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 1 hours ago.

83 stars 9.77 score 59 scripts 1 dependents

vimc

orderly:Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Maintained by Rich FitzJohn. Last updated 2 years ago.

117 stars 9.63 score 94 scripts 4 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.

hacktoberfest rmd-first

163 stars 9.45 score 35 scripts

tbates

umx:Structural Equation Modeling and Twin Modeling in R

Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.

Maintained by Timothy C. Bates. Last updated 14 days ago.

behavior-genetics genetics openmx psychology sem statistics structural-equation-modeling tutorials twin-models umx

44 stars 9.45 score 472 scripts

ropensci

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 6 months ago.

peer-reviewed reproducibility

156 stars 9.38 score 72 scripts

briencj

asremlPlus:Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 1 months ago.

asreml mixed-models

19 stars 9.37 score 200 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 5 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.

twitter twitter-api

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.

badge

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 scripts

ropensci

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.

metadata codemeta ropensci citation credit linked-data json-ld peer-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 22 hours 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.

crawler memoise rate-limiter robotstxt rvest scraper webscraping

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.

changelog git package-creation

188 stars 8.73 score 10 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.

dataimport functionalgenomics generegulation motifannotation motifdiscovery sequencematching software

50 stars 8.69 score 117 scripts 1 dependents

mrc-ide

orderly2:Orderly Next Generation

Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Maintained by Rich FitzJohn. Last updated 3 months ago.

8 stars 8.30 score 49 scripts 2 dependents

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-19 covid19 covid19-data dataset

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 8.09 score 282 scripts 2 dependents

bioc

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 8 days ago.

software reportwriting actions bioconductor biocthis github styler usethis

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 scripts

mazamascience

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 9 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.

carpentries carpentries-infrastructure carpentries-workbench lesson-template lessons markdown static-site-generator

44 stars 7.68 score 8 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.

software workflowmanagement bioconductor containers continuous-integration docker dockerhub github-actions reproducibility workflows

79 stars 7.60 score 6 scripts

ropensci

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.

appveyor continuous-integration deployment githubactions travis-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 28 days ago.

30 stars 7.47 score 5 scripts 1 dependents

bioc

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.

clustering genesetenrichment geneexpression visualization pathways kegg go microarray sequencing systemsbiology datarepresentation dataimport bioconductor bioinformatics

12 stars 7.36 score 32 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.

r-language

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.

checklist continuous-integration continuous-testing quality-assurance

19 stars 7.24 score 21 scripts 2 dependents

pik-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 8 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

ropensci

pkgcheck:rOpenSci Package Checks

Check whether a package is ready for submission to rOpenSci's peer review system.

Maintained by Mark Padgham. Last updated 18 days ago.

compliance-automation software-analysis software-checking

19 stars 7.13 score 29 scripts 1 dependents

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 10 days ago.

cpp

6 stars 7.02 score 24 scripts 1 dependents

r-lib

roxygen2md:'Roxygen' to 'Markdown'

Converts elements of 'roxygen' documentation to 'markdown'.

Maintained by Kirill Müller. Last updated 4 months ago.

documentation markdown

68 stars 7.00 score 11 scripts 2 dependents

thinkr-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.

hacktoberfest thinkr-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.

basketball college-basketball espn kenpom nba nba-analytics nba-api nba-data nba-statistics nba-stats nba-stats-api ncaa ncaa-basketball ncaa-bracket ncaa-players ncaa-ratings ncaam sportsdataverse

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 scripts

pik-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 10 hours 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 8 days ago.

rmarkdown

9 stars 6.84 score 16 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-discrimination algorithmic-fairness discrimination disparate-impact fairness fairness-ai fairness-ml machine-learning

32 stars 6.82 score 69 scripts 1 dependents

thinkr-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-research research-compendium

40 stars 6.72 score 22 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 scripts

bioc

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.

software coverage dataimport transcriptomics rnaseq preprocessing bam bigwig daspter megadepth recount2 recount3

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 13 days ago.

data-science project-management quarto

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 scripts

mazamascience

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.

packages

11 stars 6.52 score 490 scripts

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-heritage dji drone flight-planning forest-mapping litchi low-budget-uav mission-planning photogrammetry pixhawk pixhawk-controller qgroundcontrol2litchi solo survey terrain-following terrain-mapping uavs yuneec

25 stars 6.48 score 6 scripts

milesmcbain

fnmate:Create function definitions from function expressions

Convert any funcntion expression under the cursor to a definition contained in a file.

Maintained by Miles McBain. Last updated 28 days ago.

functional-programming functions

100 stars 6.48 score 9 scripts 2 dependents

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 28 days ago.

article beamer bookdown gitbook latex template thesis

23 stars 6.48 score

usaid-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

rostools

prodigenr:Research Project Directory Generator

Create a project directory structure, along with typical files for that project. This allows projects to be quickly and easily created, as well as for them to be standardized. Designed specifically with scientists in mind (mainly bio-medical researchers, but likely applies to other fields).

Maintained by Luke Johnston. Last updated 4 months ago.

devtools open-science open-source project-management reproducibility reproducible-research reproducible-science rstudio usethis

43 stars 6.33 score 25 scripts

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.

cpp

12 stars 6.27 score 77 scripts

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 21 hours 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.

javascript webpack

148 stars 6.25 score 1 scripts 2 dependents

usaid-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

ddsjoberg

starter:Starter Kit for New Projects

Get started with new projects by dropping a skeleton of a new project into a new or existing directory, initialise git repositories, and create reproducible environments with the 'renv' package. The package allows for dynamically named files, folders, file content, as well as the functionality to drop individual template files into existing projects.

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

template

27 stars 6.18 score 28 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 19 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.

rmarkdown thesis university

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

ramikrispin

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

bioc

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.

immunooncology software researchfield biologicalquestion statisticalmethod differentialexpression massspectrometry metabolomics

5 stars 6.02 score 10 scripts

jokergoo

bsub:Submitter and Monitor of the 'LSF Cluster'

It submits R code/R scripts/shell commands to 'LSF cluster' (<https://en.wikipedia.org/wiki/Platform_LSF>, the 'bsub' system) without leaving R. There is also an interactive 'shiny' application for monitoring job status.

Maintained by Zuguang Gu. Last updated 15 days ago.

software infrastructure

25 stars 6.01 score 27 scripts

ropensci

gittargets:Data Version Control for the Targets Package

In computationally demanding data analysis pipelines, the 'targets' R package (2021, <doi:10.21105/joss.02959>) maintains an up-to-date set of results while skipping tasks that do not need to rerun. This process increases speed and increases trust in the final end product. However, it also overwrites old output with new output, and past results disappear by default. To preserve historical output, the 'gittargets' package captures version-controlled snapshots of the data store, and each snapshot links to the underlying commit of the source code. That way, when the user rolls back the code to a previous branch or commit, 'gittargets' can recover the data contemporaneous with that commit so that all targets remain up to date.

Maintained by William Michael Landau. Last updated 9 months ago.

data-science data-version-control data-versioning reproducibility reproducible-research targets workflow

88 stars 5.99 score 11 scripts

ropensci

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.

review ropensci ropensci-reviews unconf unconf18

37 stars 5.97 score 28 scripts

ixpantia

ixplorer:Easy DataOps for R Users

Create and view tickets in 'gitea', a self-hosted git service <https://about.gitea.com>, using an 'RStudio' addin, and use helper functions to publish documentation and use git.

Maintained by Frans van Dunne. Last updated 5 months ago.

dataops gitea hacktoberfest

2 stars 5.94 score 5 scripts

bioc

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.

microbiome metagenomics graphandnetwork microarray patternlogic principalcomponent sequencing software visualization rnaseq immunooncology

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

keithmcnulty

neo4jshell:Querying and Managing 'Neo4J' Databases in 'R'

Sends queries to a specified 'Neo4J' graph database, capturing results in a dataframe where appropriate. Other useful functions for the importing and management of data on the 'Neo4J' server and basic local server admin.

Maintained by Keith McNulty. Last updated 3 years ago.

18 stars 5.85 score 13 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-science claims-data claims-reserving data-science insurance modelling property-casualty reserving rshiny workflow

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.

120 stars 5.80 score 15 scripts

bioc

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.

assaydomain biologicalquestion infrastructure researchfield statisticalmethod technology workflowstep network kegg

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 4 days ago.

10 stars 5.73 score 9 scripts

beanumber

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.

ggplot2 sequence-analysis traminer visualization

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 scripts

mazamascience

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 scripts

correlaid

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

rafael-ayala

openSkies:Retrieval, Analysis and Visualization of Air Traffic Data

Provides functionalities and data structures to retrieve, analyze and visualize aviation data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows retrieval of flight information, as well as aircraft state vectors.

Maintained by Rafael Ayala. Last updated 12 months ago.

11 stars 5.60 score 36 scripts

maelstrom-research

Rmonize:Support Retrospective Harmonization of Data

Functions to support rigorous retrospective data harmonization processing, 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 harmonization process, apply specified processing rules to generate harmonized data, diagnose processing errors, and summarize and evaluate harmonized outputs. The main inputs that define the processing are a DataSchema (list and definitions of harmonized variables to be generated) and Data Processing Elements (processing rules to be applied to generate harmonized variables from study-specific variables). The main outputs of processing are harmonized datasets, 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 1 years ago.

5 stars 5.58 score 51 scripts

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.

argentina estadistica openjdk

4 stars 5.57 score 124 scripts 1 dependents

tomzylkin

penppml:Penalized Poisson Pseudo Maximum Likelihood Regression

A set of tools that enables efficient estimation of penalized Poisson Pseudo Maximum Likelihood regressions, using lasso or ridge penalties, for models that feature one or more sets of high-dimensional fixed effects. The methodology is based on Breinlich, Corradi, Rocha, Ruta, Santos Silva, and Zylkin (2021) <http://hdl.handle.net/10986/35451> and takes advantage of the method of alternating projections of Gaure (2013) <doi:10.1016/j.csda.2013.03.024> for dealing with HDFE, as well as the coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010) <doi:10.18637/jss.v033.i01> for fitting lasso regressions. The package is also able to carry out cross-validation and to implement the plugin lasso of Belloni, Chernozhukov, Hansen and Kozbur (2016) <doi:10.1080/07350015.2015.1102733>.

Maintained by Joao Cruz. Last updated 2 months ago.

cpp

12 stars 5.56 score 10 scripts

bioc

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.

dnamethylation biologicalquestion preprocessing statisticalmethod normalization cpp

39 stars 5.52 score 28 scripts

ropensci

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.

openjdk

7 stars 5.50 score 18 scripts

bioc

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.

epigenetics genetics qualitycontrol chipseq multiplecomparison functionalgenomics motifdiscovery sequencematching software alignment bioconductor bioconductor-package chip-seq epigenomics interactive-report motif-enrichment-analysis

2 stars 5.48 score 6 scripts

ropensci

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 scripts

thinkr-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.

experimental

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 5 days ago.

22 stars 5.40 score 5 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 dependents

sportsdataverse

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-basketball espn espn-stats ncaa ncaa-basketball professional-basketball-data sportsdataverse wnba wnba-players wnba-stats womens-basketball

31 stars 5.40 score 54 scripts

bioc

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.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.38 score 2 scripts 2 dependents

ropensci

srr:'rOpenSci' Review Roclets

Companion package to 'rOpenSci' statistical software review project.

Maintained by Mark Padgham. Last updated 5 months ago.

compliance-automation statistical-software cpp

5 stars 5.38 score 3 scripts 2 dependents

mazamascience

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.

timeseries

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 24 days ago.

6 stars 5.26 score 4 scripts 1 dependents

ropensci

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.

cpp

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 2 days ago.

2 stars 5.23 score 9 scripts

pik-piam

modelstats:Run Analysis Tools

A collection of tools to analyze model runs.

Maintained by Anastasis Giannousakis. Last updated 12 days ago.

1 stars 5.19 score 2 scripts

bioc

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 15 days ago.

dataimport infrastructure software thirdpartyclient bioconductor-package

3 stars 5.18 score 4 scripts

ramikrispin

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

ropengov

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 11 days ago.

ropengov template github-actions pkgdown pkgdown-template

2 stars 5.16 score 3 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 dependents

usaid-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.

rstudio rstudio-addin rstudio-addins testing testthat

33 stars 5.12 score 20 scripts

pik-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 dependents

bioc

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 26 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score

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 30 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score 2 scripts

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 10 days ago.

csverse

3 stars 5.08 score 1 scripts

rcannood

qsub:Running Commands Remotely on 'Gridengine' Clusters

Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.

Maintained by Robrecht Cannoodt. Last updated 4 years ago.

9 stars 5.07 score 37 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 5 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 5 days ago.

developer-tools experimental github-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

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

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 11 days ago.

github-actions pkgdown ropenspain template yaml

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-computing utilities utility cpp

2 stars 4.95 score 2 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

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.

imd lsoa

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.

doxygen rcpp rstudio-addin

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 11 months ago.

addin buildr keyboard-shortcut rstudio-addin

15 stars 4.88 score 8 scripts

mazamascience

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.

package-manager tidyverse

122 stars 4.79 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

harrison4192

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

meztez

plumberDeploy:Plumber Deployment

Gives the ability to automatically deploy a plumber API from R functions on 'DigitalOcean' and other cloud-based servers.

Maintained by Bruno Tremblay. Last updated 9 months ago.

55 stars 4.74 score 6 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.

dataset

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-template research-compendium workflow

175 stars 4.70 score 57 scripts

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.

hacktoberfest hacktoberfest2021 mail mailer sendgrid

23 stars 4.66 score 10 scripts

bioc

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.

dnamethylation methylationarray transcription genomewideassociation software openjdk

4.65 score 14 scripts

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.

forecasting machine-learning predictive-modeling statistical-learning time-series time-series-forecasting uncertainty-quantification cpp

21 stars 4.63 score 51 scripts

pik-piam

limes:The liMES R package

Contains the LIMES-specific routines for data and model output manipulation.

Maintained by Sebastian Osorio. Last updated 12 days ago.

1 stars 4.63 score 5 scripts

mrchypark

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.

hacktoberfest hacktoberfest2021

7 stars 4.63 score 121 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-republic datasets open-data

8 stars 4.60 score 6 scripts

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

pik-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 12 hours ago.

tada text-mining

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 9 months ago.

7 stars 4.54 score 5 scripts

ropensci

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 17 days ago.

dashboard software-metrics

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.

rhdf5 data-pipeline fair

4 stars 4.52 score 11 scripts

inbo

INBOmd:Markdown Templates for INBO

Several templates to generate reports, presentations and posters.

Maintained by Thierry Onkelinx. Last updated 1 years ago.

bookdown rmarkdown xelatex

12 stars 4.52 score 11 scripts

pik-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 2 days ago.

1 stars 4.49 score 13 scripts

permaverse

nevada:Network-Valued Data Analysis

A flexible statistical framework for network-valued data analysis. It leverages the complexity of the space of distributions on graphs by using the permutation framework for inference as implemented in the 'flipr' package. Currently, only the two-sample testing problem is covered and generalization to k samples and regression will be added in the future as well. It is a 4-step procedure where the user chooses a suitable representation of the networks, a suitable metric to embed the representation into a metric space, one or more test statistics to target specific aspects of the distributions to be compared and a formula to compute the permutation p-value. Two types of inference are provided: a global test answering whether there is a difference between the distributions that generated the two samples and a local test for localizing differences on the network structure. The latter is assumed to be shared by all networks of both samples. References: Lovato, I., Pini, A., Stamm, A., Vantini, S. (2020) "Model-free two-sample test for network-valued data" <doi:10.1016/j.csda.2019.106896>; Lovato, I., Pini, A., Stamm, A., Taquet, M., Vantini, S. (2021) "Multiscale null hypothesis testing for network-valued data: Analysis of brain networks of patients with autism" <doi:10.1111/rssc.12463>.

Maintained by Aymeric Stamm. Last updated 4 months ago.

openblas cpp

6 stars 4.48 score 7 scripts

bioc

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.

infrastructure reportwriting software

3 stars 4.48 score 4 scripts

dnme-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.

argentina estadistica

5 stars 4.47 score 79 scripts 1 dependents

certara

Certara.R:Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara

A convenient set of wrapper functions to install pharmacometric packages and Shiny applications developed by Certara PMX and Integrated Drug Development (iDD). The functions ensure the successful installation of packages from non-standard repositories.

Maintained by James Craig. Last updated 5 months ago.

pharmacometrics r-pkg

14 stars 4.45 score 2 scripts

hubverse-org

hubDevs:Utilities for Creating and Standardising Hubverse Packages

What the package does (one paragraph).

Maintained by Anna Krystalli. Last updated 3 months ago.

hubverse

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.

miscellaneous cpp

1 stars 4.40 score 50 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

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-analytics moodle moodle-data

5 stars 4.40 score 9 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 scripts

helske

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-change pacta pactaverse sustainable-finance

1 stars 4.36 score 11 scripts 1 dependents

thinkr-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.

proteomics regression differentialexpression biomedicalinformatics genetarget geneexpression network

2 stars 4.30 score 2 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

bioc

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.

software reportwriting

4.30 score 10 scripts

kserkcho

SCEM:Splitting-Coalescence-Estimation Method

We introduce improved methods for statistically assessing birth seasonality and intra-annual variation. The first method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. One can use the function SCEM() to implement this method. The second method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits_OLS(), while makeFits_initial() is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach. One can use the function makeFits() to generate parametric birth seasonality estimates using either initialization. Detailed description can be found here: Chazin Hannah, Soudeep Deb, Joshua Falk, and Arun Srinivasan. (2019) "New Statistical Approaches to Intra-Individual Isotopic Analysis and Modeling Birth Seasonality in Studies of Herd Animals." <doi:10.1111/arcm.12432>.

Maintained by Kyung Serk Cho. Last updated 4 years ago.

scem

4.30 score 3 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 16 days ago.

2 stars 4.27 score 47 scripts

pacificcommunity

condor:Interact with 'Condor' from R via SSH

Interact with 'Condor' from R via SSH connection. Files are first uploaded from user machine to submitter machine, and the job is then submitted from the submitter machine to 'Condor'. Functions are provided to submit, list, and download 'Condor' jobs from R. 'Condor' is an open source high-throughput computing software framework for distributed parallelization of computationally intensive tasks.

Maintained by Arni Magnusson. Last updated 5 months ago.

htcondor ofp sam tool

5 stars 4.26 score 24 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 25 days ago.

3 stars 4.26 score

opencasestudies

OCSdata:Download Data from the 'Open Case Studies' Repository

Provides functions to access and download data from the 'Open Case Studies' <https://www.opencasestudies.org/> repositories on 'GitHub' <https://github.com/opencasestudies>. Different functions enable users to grab the data they need at different sections in the case study, as well as download the whole case study repository. All the user needs to do is input the name of the case study being worked on. The package relies on the httr::GET() function to access files through the 'GitHub' API. The functions usethis::use_zip() and usethis::create_from_github() are used to clone and/or download the case study repositories. See <https://github.com/opencasestudies/OCSdata/blob/master/README.md> for instructions and examples. To cite an individual case study, please see the 'README' file in the respective case study repository: <https://github.com/opencasestudies/ocs-bp-rural-and-urban-obesity> <https://github.com/opencasestudies/ocs-bp-air-pollution> <https://github.com/opencasestudies/ocs-bp-vaping-case-study> <https://github.com/opencasestudies/ocs-bp-opioid-rural-urban> <https://github.com/opencasestudies/ocs-bp-RTC-wrangling> <https://github.com/opencasestudies/ocs-bp-RTC-analysis> <https://github.com/opencasestudies/ocs-bp-youth-disconnection> <https://github.com/opencasestudies/ocs-bp-youth-mental-health> <https://github.com/opencasestudies/ocs-bp-school-shootings-dashboard> <https://github.com/opencasestudies/ocs-bp-co2-emissions> <https://github.com/opencasestudies/ocs-bp-diet>.

Maintained by Carrie Wright. Last updated 8 months ago.

data-science public-health

1 stars 4.20 score 32 scripts

ingorohlfing

qcapower:Estimate Power and Required Sample Size in QCA

Researchers working with Qualitative Comparative Analysis (QCA) can use the package to estimate power of a sufficient term using permutation tests. A term can be anything: A condition, conjunction or disjunction of any combination of these. The package further allows users to plot the estimation results and to estimate the number of cases required to achieve a certain level of power, given a prespecified null and alternative hypothesis. Reference for the article introducing power estimation for QCA is: Rohlfing, Ingo (2018) <doi:10.1017/pan.2017.30> (ungated version: <doi:10.17605/OSF.IO/PC4DF>).

Maintained by Ingo Rohlfing. Last updated 5 years ago.

3 stars 4.18 score 7 scripts

joshualerickson

whitewater:Parallel Processing Options for Package 'dataRetrieval'

Provides methods for retrieving United States Geological Survey (USGS) water data using sequential and parallel processing (Bengtsson, 2022 <doi:10.32614/RJ-2021-048>). In addition to parallel methods, data wrangling and additional statistical attributes are provided.

Maintained by Josh Erickson. Last updated 9 months ago.

8 stars 4.16 score 36 scripts

bioc

BUMHMM:Computational pipeline for computing probability of modification from structure probing experiment data

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Maintained by Alina Selega. Last updated 5 months ago.

immunooncology geneticvariability transcription geneexpression generegulation coverage genetics structuralprediction transcriptomics bayesian classification featureextraction hiddenmarkovmodel regression rnaseq sequencing

4.15 score 14 scripts

corradolanera

depigner:A Utility Package to Help you Deal with "Pignas"

Pigna [_pìn'n'a_] is the Italian word for pine cone. In jargon, it is used to identify a task which is boring, banal, annoying, painful, frustrating and maybe even with a not so beautiful or rewarding result, just like the obstinate act of trying to challenge yourself in extracting pine nuts from a pine cone, provided that, in the end, you will find at least one inside it. Here you can find a backpack of functions to be used to solve small everyday problems of coding or analyzing (clinical) data, which would be normally solved using quick-and-dirty patches. You will be able to convert 'Hmisc' and 'rms' summary()es into data.frames ready to be rendered by 'pander' and 'knitr'. You can access easy-to-use wrappers to activate essential but useful progress bars (from 'progress') into your loops or functionals. Easy setup and control Telegram's bots (from 'telegram.bot') to send messages or to divert error messages to a Telegram's chat. You also have some utilities helping you in the development of packages, like the activation of the same user interface of 'usethis' into your package, or call polite functions to ask a user to install other packages. Finally, you find a set of thematic sets of packages you may use to set up new environments quickly, installing them in a single call.

Maintained by Corrado Lanera. Last updated 2 years ago.

hmisc pigne rms telegram

3 stars 4.14 score 93 scripts

inbo

protocolhelper:Helper Functions to Manage Protocols

Helper functions to manage INBO protocols.

Maintained by Hans Van Calster. Last updated 10 days ago.

5 stars 4.09 score 55 scripts

feddelegrand7

rfold:Working with many R Folders Within an R Package

Allows developers to work with many R folders inside a package. It offers functionalities to transfer R scripts (saved outside the R folder) into the R folder while making additional checks.

Maintained by Mohamed El Fodil Ihaddaden. Last updated 1 years ago.

23 stars 4.06 score 2 scripts

mbatsaris

populR:Population Downscaling Using Areal Interpolation

Given a set of source zone polygons such as census tracts or city blocks alongside with population counts and a target zone of incogruent yet superimposed polygon features (such as individual buildings) populR transforms population counts from the former to the latter using Areal Interpolation methods.

Maintained by Marios Batsaris. Last updated 2 years ago.

2 stars 4.04 score 11 scripts

bioc

rifiComparative:'rifiComparative' compares the output of rifi from two different conditions.

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Maintained by Loubna Youssar. Last updated 5 months ago.

rnaseq differentialexpression generegulation transcriptomics microarray software

4.00 score

hubverse-org

hubverse:Easily Install and Load the 'hubverse'

A collection of packages that enables collaborative modeling exercises through a unified framework for aggregating, visualizing, and evaluating forecasts. This package is designed to make it easy to install and load multiple 'hubverse' packages in a single step. Learn more at <https://hubverse.io/en/latest/index.html>.

Maintained by Li Shandross. Last updated 6 months ago.

4.00 score 5 scripts

covid19r

covid19swiss:COVID-19 Cases in Switzerland and Principality of Liechtenstein

Provides a daily summary of the Coronavirus (COVID-19) cases in Switzerland cantons and Principality of Liechtenstein. Data source: Specialist Unit for Open Government Data Canton of Zurich <https://www.zh.ch/de/politik-staat/opendata.html>.

Maintained by Rami Krispin. Last updated 4 years ago.

4.00 score 8 scripts

acribbs

siteymlgen:Automatically Generate _site.yml File for 'R Markdown'

The goal of 'siteymlgen' is to make it easy to organise the building of your 'R Markdown' website. The init() function placed within the first code chunk of the index.Rmd file of an 'R' project directory will initiate the generation of an automatically written _site.yml file. 'siteymlgen' recommends a specific naming convention for your 'R Markdown' files. This naming will ensure that your navbar layout is ordered according to a hierarchy.

Maintained by Adam Cribbs. Last updated 4 years ago.

2 stars 4.00 score 5 scripts

personalizedtransplantcare

banffIT:Automatize Diagnosis Standardized Assignation Using the Banff Classification

Assigns standardized diagnoses using the Banff Classification (Category 1 to 6 diagnoses, including Acute and Chronic active T-cell mediated rejection as well as Active, Chronic active, and Chronic antibody mediated rejection). The main function considers a minimal dataset containing biopsies information in a specific format (described by a data dictionary), verifies its content and format (based on the data dictionary), assigns diagnoses, and creates a summary report. The package is developed on the reference guide to the Banff classification of renal allograft pathology Roufosse C, Simmonds N, Clahsen-van Groningen M, et al. A (2018) <doi:10.1097/TP.0000000000002366>. The full description of the Banff classification is available at <https://banfffoundation.org/>.

Maintained by Guillaume Fabre. Last updated 11 months ago.

4.00 score

tjmahr

wisclabmisc:Tools to Support the 'WiscLab'

A collection of 'R' functions for use (and re-use) across 'WiscLab' projects. These are analysis or presentation oriented functions--that is, they are not for data reading or data cleaning.

Maintained by Tristan Mahr. Last updated 9 days ago.

4.00 score 4 scripts

cran

YEAB:Analyze Data from Analysis of Behavior Experiments

Analyze data from behavioral experiments conducted using 'MED-PC' software developed by Med Associates Inc. Includes functions to fit exponential and hyperbolic models for delay discounting tasks, exponential mixtures for inter-response times, and Gaussian plus ramp models for peak procedure data, among others. For more details, refer to Alcala et al. (2023) <doi:10.31234/osf.io/8aq2j>.

Maintained by Emmanuel Alcala. Last updated 2 months ago.

4.00 score

usaid-oha-si

selfdestructin5:Creates SI OHA Mission Director Briefers

Creates a series of data frames that can be passed to a gt() to create the PEPFAR summary tables.

Maintained by Tim Essam. Last updated 1 months ago.

1 stars 3.98 score 21 scripts

repboxr

repboxDB:Functions for exported repbox data

Functions for exported repbox data

Maintained by Sebastian Kranz. Last updated 4 months ago.

3.91 score 8 scripts 9 dependents

biogenies

CancerGram:Prediction of Anticancer Peptides

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI. The CancerGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/BioGenies/CancerGramModel>. For more information see: Burdukiewicz et al. (2020) <doi:10.3390/pharmaceutics12111045>.

Maintained by Michal Burdukiewicz. Last updated 4 years ago.

anticancer-peptides bioinformatics k-mer n-gram peptide-identification random-forests

4 stars 3.90 score 3 scripts

richelbilderbeek

pureseqtmr:Predict Transmembrane Protein Topology

Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.

Maintained by Richèl J.C. Bilderbeek. Last updated 2 years ago.

cpp

1 stars 3.90 score 16 scripts