awesome-reproducible-research
A curated list of reproducible research case studies, projects, tutorials, and media
https://github.com/leipzig/awesome-reproducible-research
Last synced: 4 days 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/).
- DVC - DVC tracks machine learning models and data sets
- DataLad - Git-based versioning for data and provenance
- Overture - Portal, query interface, visualization and schema framework that powers ICGC, KFDC, GDC
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Courses
- Coursera Reproducible Research - Roger Peng et al JHU. Very popular course.
- edX Principles, Statistical and Computational Tools for Reproducible Science - John Quackenbush et al Harvard
- Reproducible research: methodological principles for transparent science - Beginner level. Note taking, version control, notebooks, reproducible data analysis. Bilingual English/French.
- Tools for Reproducible Research - Karl Broman UW, includes resources page
- R-DAVIS - Student-developed computer literacy and data course in R
- Reproducible-Science-Curriculum - A curriculum for teaching reproducible computational science bootcamps
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Development Resources
- CRAN Task View - Reproducible Research - packages relevant to RCR in R
- liftr - persistent reproducible reporting through containerized R Markdown documents
- orderly - R package that automates writing reproducible analyses
- Reproducible Builds - a set of software development practices that create an independently-verifiable path from source to binary code
- mlf-core - Framework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost
- orderly - R package that automates writing reproducible analyses
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Literature tools
- 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.
- 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.
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Books
- Reproducible Research with R and R Studio 2013
- Implementing Reproducible Research 2014 - Describes projects: Sumatra, Vistrails, CDE, SOLE, JUMBO, CML, knitr. Content available on OSF.
- 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
- Reproducibility: Principles, Problems, Practices, and Prospects
- The Turing Way: A Handbook for Reproducible Data Science 2020
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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
- ReplicationDatabase - 1211 replication findings on 333 psychology studies
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Data Repositories
- Data Dryad - curated, metadata-centric, focused on articles associated with published artices, $120 submission fee (various waivers available)
- Figshare - 20 GB of free private space, unlimited public space, >2M articles, >5k projects
- Zenodo - Allows embargoed, restricted access, metadata support. 50GB limit.
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Organizations
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Siepel lab
- CASCaD - Certification Agency for Scientific Code and Data. Issues reproducibility certificates.
- ResearchObject.org - RO specifications and publications
- BioCompute - BCO specs
- rOpenSci - Tools, conferences, and education
- 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.
- repliCATS project - Estimating the replicability of research in the social sciences. [Paper](https://osf.io/preprints/metaarxiv/2pczv/)
- CODECHECK - community for checking executability of scientific preprints and papers
- Reproducibility for Everyone - Community-led reproducibility workshops
- 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
- 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
- FORRT - Framework for Open and Reproducible Research Training advancing research transparency, reproducibility, rigor, and ethics through pedagogical reform and meta-scientific research
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Exemplar Portals
- Jupyter Gallery - Gallery of interesting Jupyter notebooks
- Papers With Code - ML papers with code
- Codeocean - A gallery of cloud-based containers with reproducible analyses
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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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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. [Preprint](https://doi.org/10.1101/2020.06.24.167353)
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Awesome Lists
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Siepel lab
- Awesome Docker - Everything related to the Docker containerization system
- Awesome R - Section on RR tools
- Awesome Public Datasets - A topic-centric list of HQ open datasets
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Programming Languages
Categories
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Keywords
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