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95 search results found

Drake ⭐ 1,332

An R-focused pipeline toolkit for reproducibility and high-performance computing

Gtsummary ⭐ 892

Presentation-Ready Data Summary and Analytic Result Tables

Targets ⭐ 860

Function-oriented Make-like declarative workflows for R

Render bits of R code for sharing, e.g., on GitHub or StackOverflow.

Rrtools ⭐ 619

rrtools: Tools for Writing Reproducible Research in R

An R package implementing the UMAP dimensionality reduction method.

Biomartr ⭐ 198

Genomic Data Retrieval with R

Statcheck ⭐ 162

A spellchecker for statistics

🐳 Containerize R Markdown documents for continuous reproducibility

Batchtools ⭐ 158

Tools for computation on batch systems

Checkpoint ⭐ 150

Install R packages from snapshots on checkpoint-server

Datapackager ⭐ 137

An R package to enable reproducible data processing, packaging and sharing.

🐳 A Docker image builder for researchers

Starters ⭐ 123

R Package 📦 for initializing projects for various R activities 🔩

Tarchetypes ⭐ 108

Archetypes for targets and pipelines

Ezknitr ⭐ 107

Avoid the typical working directory pain when using 'knitr'

Reproducible Research ⭐ 95

A Reproducible Data Analysis Workflow with R Markdown, Git, Make, and Docker

Targets Tutorial ⭐ 90

Short course on the targets R package

Gittargets ⭐ 69

Data version control for reproducible analysis pipelines in R with {targets}.

🐶 (Re)constructing R computational environments

Prepare reproducible R Markdown posters

Targets Shiny ⭐ 60

Example Shiny app containing a targets pipeline.

Drake Examples ⭐ 58

Example workflows for the drake R package

The user manual for the drake R package

Rworkflows ⭐ 50

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.

👻 Capture the spirit of your ggplot call

Reprohack Hq ⭐ 46

ReproHack Headquarters

Targets Minimal ⭐ 45

A minimal example data analysis project with the targets R package

creating optimal conditions for reproducibility

Stantargets ⭐ 42

Reproducible Bayesian data analysis pipelines with targets and cmdstanr

Reproducible ⭐ 40

A set of tools for R that enhance reproducibility beyond package management

Prodigenr ⭐ 36

Project directory generator R package

Snakemake Econ R ⭐ 35

reproducible research project template for R using Renv and snakemake with an econ application

Rr Organization1 ⭐ 35

The Organization lesson for the Reproducible Science Curriculum

Software Dev ⭐ 33

Coding Standards for the USC Biostats group

Reproducibilidad ⭐ 30

Reproducible Science: what, why, how

📄 R package: Dynamic generation of scientific reports

Dependency Management with roxygen-style Comments

Reproducibility Via Singularity ⭐ 25

A demo and tutorial for how to use git and singularity to make your research more portable and reproducible

Researchcompendium ⭐ 24

NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

2020_wilk_covid ⭐ 23

Reproducibility repository accompanying Wilk, Rustagi, Zhao, et al. "A single-cell atlas of the peripheral immune response to severe COVID-19"

Reproducibility_in_plant_pathology ⭐ 20

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

A workshop on Data

Repro_web_stack ⭐ 19

The stack I use to make reproducible reports of my statistical analyses

Mlr3 Learndrake ⭐ 18

Template for using mlr3 with drake

Genus 2017 ⭐ 17

Reproduce "Decomposition of regional convergence in population aging across Europe. Genus, 73(1), 2"

Datacleanr ⭐ 17

Interactive and Reproducible Data Cleaning

User manual of the targets R pacakge

Targetsketch ⭐ 15

Sketch a pipeline of targets in an interactive web app

R package | May All Data be Reproducible and Transparent (MADRaT)

Reproducible Research Ctv ⭐ 14

**Archived** CRAN Task View: Reproducible Research

Aea De Guidance ⭐ 14

Unofficial guidance for authors wishing to create data and code supplements, and for replicators

Chromatographr ⭐ 11

Toolset for the reproducible analysis of chromatography data in R (HPLC-DAD/UV, GC-FID).

Mandrake ⭐ 11

📖🐉- Bring reading the manual 📖 closer to your drake 🐉 workflow 🔥

A place to update and store my R configuration

Import spectral data and related metadata in R

Targets Stan ⭐ 11

An example project to validate a Stan model in a targets pipeline

Rr Automation ⭐ 10

Resources for automation tutorials

R package to simplify workflows of D6 research projects. The package provides utilities to set up a standardized folder structure and version control, and Rmarkdown templates and rendering functionality for a reproducible workflow.

Repromonkey ⭐ 10

🐒 A Reproducibility Chaos Monkey

Reproducible_bioinformatics ⭐ 10

Workshop material for BioC Asia 2019

Hexbin_qld ⭐ 10

An example of hexbinning for mapping using {h3jsr}, {dplyr}, {sf}, and {mapdeck}

Aroma.affymetrix ⭐ 9

🔬 R package: Analysis of Large Affymetrix Microarray Data Sets

Ci Images ⭐ 9

Insights Engineering Container Images

Jagstargets ⭐ 9

Reproducible Bayesian data analysis pipelines with targets and JAGS

Rr Version Control ⭐ 8

Reproducible Science Curriculum Lesson for Version Control

Introduction materials for Reproducible Research Curriculum

An R package for reproducible research. Analyze your experimental data and generate HTML and PDF reports.

Codename Generation for Organizations, People, Projects, and Whatever Else

Rr Literate Programming ⭐ 7

Repository for lesson materials on Literate Programming

Inclusion of processed cell metadata improves single cell sequencing analysis reproducibility and accessibility

Docker Reproducibility Example ⭐ 7

Example of providing a docker container for reproducible analyses

Data Is Present ⭐ 7

This project offered free activities to practise reproducible data presentation. Pablo Bernabeu organised these events in the context of a Software Sustainability Institute Fellowship.

[R package]: Datasets from "Applied Logistic Regression" by Hosmer D.W., Lemeshow S. and Sturdivant X.

Reprochecklist ⭐ 7

#eLifeAmbassadors reviewer's checklist for assessing reproducibility of computational methods in life science publications

Scriptgloss ⭐ 7

dynamically reconstruct static code for shiny outputs

2018 11 06 Rladies Talk ⭐ 7

Slides from a talk given at the R-Ladies NYC meetup

Codecheck ⭐ 7

R package assistant for conducting a CODECHECK

Shinyr Knowledge Repo ⭐ 7

The shinyR curated knowledge sharing platform

Source code for talk slides on reproducibility, research data management and open science

Targets Keras ⭐ 7

An example Keras pipeline with the targets R package

Aid Steno Researchers Who Work on the UKB RAP.

1000 Tools Paper ⭐ 6

Code and analysis for the 1000 tools paper

Superheat Examples ⭐ 6

Examples available at:

a lightweight method of creating R package dependencies for a project OR "baby steps to reproducibility"

Opensensmapr ⭐ 6

R client for opensensemap.org

Drake Egg Rap ⭐ 5

🦆🥚🎤 Demo: {drake} for reproducible pipelines with UK government stats reports

R package to evaluate reproducibility of Hi-C data

R package for Hidden Markov Models with t emissions

Targets Design ⭐ 5

targets R package design specification

Tropical Data Analysis Public ⭐ 5

Tropical Data standard analysis code combining v1 and v2 methodologies, coded for public use by Ana Bakhtiari ([email protected])

Single-Cell Reproducibility Across Donors

Ctv Computational Environments ⭐ 5

A CRAN task view for computational environments and reproducibility

2019 05 14_reproducibility ⭐ 5

🏫 Materials for talk/demonstration on reproducibility in R, given May 14, 2019 at the Utah County RUG

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