awesome-reproducible-research
A curated list of reproducible research case studies, projects, tutorials, and media
https://github.com/leipzig/awesome-reproducible-research
Last synced: about 4 hours ago
JSON representation
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Scientific Data Management Systems
- Fairly Toolset - Tools for preparing, publishing and downloading datasets from research data repositories directly into computing environments. It provides integration with [Zenodo](https://fairly.readthedocs.io) and [Figshare](https://figshare.com/).
- Overture - Portal, query interface, visualization and schema framework that powers ICGC, KFDC, GDC
- DVC - DVC tracks machine learning models and data sets
- DataLad - Git-based versioning for data and provenance
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Courses
- Tools for Reproducible Research - Karl Broman UW, includes resources page
- Coursera Reproducible Research - Roger Peng et al JHU. Very popular course.
- R-DAVIS - Student-developed computer literacy and data course in R
- edX Principles, Statistical and Computational Tools for Reproducible Science - John Quackenbush et al Harvard
- R for Reproducible Scientific Analysis - Software Carpentry workshop primer using Gapminder data
- AMIA2019 - Pragmatic RR for Analysis, Dissemination and Publication
- PSU-PSY525 - Transparent, Open, and Reproducible Research Practices in the Social and Behavioral Sciences
- edX Principles, Statistical and Computational Tools for Reproducible Science - John Quacken et al Harvard
- Reproducible research: methodological principles for transparent science - Beginner level. Note taking, version control, notebooks, reproducible data analysis. Bilingual English/French.
- Monash-RRR - Reproducible Research in R workshop tutorial
- OSU-OSRR - An open science and reproducible research course targeted at organismal ecologists
- Reproducible-Science-Curriculum - A curriculum for teaching reproducible computational science bootcamps
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Development Resources
- orderly - R package that automates writing reproducible analyses
- mlf-core - Framework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost
- BILN - a lightweight, "black box" flight recorder for bioinformatics experiments
- CRAN Task View - Reproducible Research - packages relevant to RCR in R
- liftr - persistent reproducible reporting through containerized R Markdown documents
- Reproducible Builds - a set of software development practices that create an independently-verifiable path from source to binary code
- repo - provenance framework package
- orderly - R package that automates writing reproducible analyses
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Books
- Reproducible Research with R and R Studio 2013
- The Practice of Reproducible Research 2017 - 31 first person case narratives and intro chapters
- Dynamic Documents with R and knitr 2015
- Reproducibility and Replicability in Science
- Reproducible Research with R and R Studio 2013
- The Practice of Reproducible Research 2017 - 31 first person case narratives and intro chapters
- The Turing Way: A Handbook for Reproducible Data Science 2020
- Dynamic Documents with R and knitr 2015
- Implementing Reproducible Research 2014 - Describes projects: Sumatra, Vistrails, CDE, SOLE, JUMBO, CML, knitr. Content available on OSF.
- Reproducibility and Replicability in Science
- The Turing Way: A Handbook for Reproducible Data Science 2020
- Reproducibility: Principles, Problems, Practices, and Prospects
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Databases
- ReplicationWiki - Database for empirical studies with information about methods, data and software used, availability of replication material and whether replications, corrections or retractions are known. Mostly focused on social sciences.
- ReproCrawl
- ReplicationWiki - Database for empirical studies with information about methods, data and software used, availability of replication material and whether replications, corrections or retractions are known. Mostly focused on social sciences.-->
- ReplicationDatabase - 1211 replication findings on 333 psychology studies
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Journals
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Ontologies
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Siepel lab
- FAIRsharing - standards, databases, and policies
- BioPortal - 660 biomedical ontologies
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Organizations
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Siepel lab
- ResearchObject.org - RO specifications and publications
- CUrating for REproducibility - curation of research and code for digital preservation
- Michigan Institute for Data Science Reproducibility Hub - [reproducibility challenge](https://hdsr.mitpress.mit.edu/pub/mlconlea/release/1) manuscripts & presentations
- rOpenSci - Tools, conferences, and education
- repliCATS project - Estimating the replicability of research in the social sciences. [Paper](https://osf.io/preprints/metaarxiv/2pczv/)
- BioCompute - BCO specs
- Reproducibility for Everyone - Community-led reproducibility workshops
- Michigan Institute for Data Science Reproducibility Hub
- Reproducibility challenge
- World Bank Reproducible Research Initiative - Institutional framework transforming development economics through transparent science and reproducible research practices
- FORRT - Framework for Open and Reproducible Research Training advancing research transparency, reproducibility, rigor, and ethics through pedagogical reform and meta-scientific research
- pyOpenSci - Promotes open and reproducible research through peer-review of scientific Python packages
- Replication Network - Furthering the practice of replication in economics. Econ replication database.
- ReproHack - 1-day reproducibility hackathons held worldwide
- CODECHECK - community for checking executability of scientific preprints and papers
- CASCaD - Certification Agency for Scientific Code and Data. Issues reproducibility certificates.
- OpenMKT - transparency and quality of marketing research published in academic journals
- Many Co-Authors - online platform designed to collect and share information on the provenance and availability of the data for all articles co-authored by Francesca Gino
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Literature tools
- Ripeta - Ripeta quickly scans research manuscripts or articles to identify and record key reproducibility variables, such as data availability, code acknowledgements, and research analysis methods.
- Scite - Citation statement AI for discovering and evaluating scientific articles
- SciScore - SciScore methods sections for a variety of rigor criteria and analyzes sentences that contain research resources (antibodies, cell lines, plasmids and software tools) and determines how uniquely identifiable that resource is based off of the provided metadata.
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Exemplar Portals
- Codeocean - A gallery of cloud-based containers with reproducible analyses
- Jupyter Gallery - Gallery of interesting Jupyter notebooks
- NARPS - Code related to Neuroimaging Analysis Replication and Prediction Study
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Awesome Lists
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Siepel lab
- Awesome Public Datasets - A topic-centric list of HQ open datasets
- Awesome Pipeline - So many pipelines frameworks
- Awesome Docker - Everything related to the Docker containerization system
- Awesome R - Section on RR tools
- Awesome Reproducible R - RRR tools
- Awesome Bioinformatics Benchmarks - Benchmarks are a related aspect of robustness testing
- Awesome Open Science - Resources, data, tools, and scholarship
- Awesome Semantic Web - Semantic web and linked data resources.
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Data Repositories
- Zenodo - Allows embargoed, restricted access, metadata support. 50GB limit.
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Minimal Standards
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Siepel lab
- STORMS - Strengthening The Organization and Reporting of Microbiome Studies (STORMS) is a checklist for reporting on human microbiome studies. [Paper](https://doi.org/10.1038/s41591-021-01552-x)
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Programming Languages
Categories
Sub Categories
Keywords
awesome-list
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awesome
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docker-swarm
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tools
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awesome-public-datasets
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datasets
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opendata
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workflow
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owl
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r2rml
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rdf
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semantic-web
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sparql
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docker-security
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docker-registry
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docker-monitoring
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docker-machine
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docker-image
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docker-environment
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open-data
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