readme.md

Awesome Reproducible Research

A curated list of reproducible research case studies, projects, tutorials, and media

Contents

• Case studies
• Ad-hoc reproductions
• Theory papers
• Tool reviews
• Courses
• Development Resources
• User tools
• Books
• Databases
• Data Repositories
• Exemplar Portals
• Runnable Papers
• Journals
• Ontologies
• Minimal Standards
• Organizations
• Awesome Lists

Case studies

The term "case studies" is used here in a general sense to describe any study of reproducibility. A reproduction is an attempt to arrive at comparable results with identical data using computational methods described in a paper. A refactor involves refactoring existing code into frameworks and other reproducibility best practices while preserving the original data. A replication involves generating new data and applying existing methods to achieve comparable results. A robustness test applies various protocols, workflows, statistical models or parameters to a given data set to study their effect on results, either as a follow-up to an existing study or as a "bake-off". A census is a high-level tabulation conducted by a third party. A survey is a questionnaire sent to practitioners. A case narrative is an in-depth first-person account. An independent discussion utilizes a secondary independent author to interpret the results of a study as a means to improve inferential reproducibility.

Study	Field	Approach	Size
Glasziou et al 2008	Medicine	Census	80 studies
Baggerly & Coombes 2009	Cancer biology	Refactor	8 studies
Hothorn et al. 2009	Biostatistics	Census	56 studies
Ioannidis et al 2009	Genetics	Reproduction	18 studies
Anda et al 2009	Software engineering	Replication	4 companies
Vandewalle et al 2009	Signal processing	Census	134 papers
Prinz 2011	Biomedical sciences	Survey	23 PIs
Horthorn & Leisch 2011	Bioinformatics	Census	100 studies
Begley & Ellis 2012	Cancer biology	Replication	53 studies
Collberg et al 2014 Collberg & Proebsting 2016	Computer science	Census	613 papers
OSC 2015	Psychology	Replication	100 studies
Bandrowski et al 2015	Biomedical sciences	Census	100 papers
Patel et al 2015	Epidemiology	Robustness test	417 variables
Chang et al 2015	Economics	Reproduction	67 papers
Iqbal et al 2016	Biomedical sciences	Census	441 papers
Baker 2016	Science	Survey	1,576 researchers
Névéol et al 2016	NLP	Replication	3 studies
Reproducibility Project 2017	Cancer biology	Replication	9 studies
Vasilevsky et al 2017	Biomedical sciences	Census	318 journals
Kitzes et al 2017	Science	Case narrative	31 PIs
Barone et al 2017	Biological sciences	Survey	704 PIs
Kim & Dumas 2017	Bioinformatics	Refactor	1 study
Camerer 2017	Economics	Replication	18 studies
Olorisade 2017	Machine learning	Census	30 studies
Strupler & Wilkinson 2017	Archaeology	Case narrative	1 survey
Danchev et al 2017	Comparative toxicogenomics	Census	51,292 claims in 3,363 papers
Kjensmo & Gundersen 2018	Artificial intelligence	Census	400 papers
Gertler et al 2018	Economics	Census	203 papers
Stodden et al 2018	Computational science	Reproduction	204 papers, 180 authors
Madduri et al 2018	Genomics	Case narrative	1 study
Camerer et al 2018	Social sciences	Replication	21 papers
Silberzahn et al 2018	Psychology	Robustness test	One data set, 29 analyst teams
Boulesteix et al 2018	Medicine and health sciences	Census	30 papers
Eaton et al 2018	Microbiome immuno oncology	Replication	1 paper
Vaquero-Garcia et al 2018	Bioinformatics	Refactor and test of robustness	1 paper
Wallach et al 2018	Biomedical Sciences	Census	149 papers
Miller et al 2018	Bioinformatics	Synthetic replication & refactor	1 paper
Konkol et al 2018	Geosciences	Survey, Reproduction	146 scientists, 41 papers
Rahtz 2018	Reinforcement Learning	Reproduction, case narrative	1 paper
Stodden et al 2018	Computational physics	Census	306 papers
AlNoamany & Borghi 2018	Science & Engineering	Survey	215 participants
Li et al 2018	Nephrology	Robustness test	1 paper
Chen 2018	Social sciences & other	Census	810 Dataverse studies
Trisovic et al 2021	Social sciences & other	Census, Survey	2109 replication datasets
Nüst et al 2018	GIScience/Geoinformatics	Census, Survey	32 papers, 22 participants
Raman et al 2018	Genomics	Robustness test	8 studies
Stagge et al 2019	Geosciences	Survey	360 papers
Bizzego et al 2019	Deep learning	Robustness test	1 analysis
Madduri et al 2019	Genomics	Case narrative	1 analysis
Mammoliti et al 2019	Pharmacogenomics	Case narrative	2 analyses
Allen & Mehler 2019	Biomedical sciences and Psychology	Census	127 registered reports
Pimentel et al 2019	All	Census	1,159,166 Jupyter notebooks
Fergusson et al 2019	Virology	Census	236 papers
Vlisides et al 2019 Sieber et al 2019	Anaesthesia	Indepedent discussion	1 study
Bakker et al 2019	Psychology	Replication	1 paper
Niepel et al 2019	Cell pharmacology	Robustness test	5 labs
Dacrema et al 2019	Machine learning	Reproduction	18 conference papers
Eran et al 2019	Experimental archaeology	Replication	1 theory
Rauh et al 2019	Neurology	Census	202 papers
Sætrevik & Sjåstad 2019	Psychology	Replication	2 experiments
Feng et al. 2019	Ecology and Evolution	Census	163 papers
Botvinik-Nezer et al. 2019	Neuroimaging	Robustness test	1 data set, 70 teams
Klein et al. 2019	Psychology	Replication	1 experiment, 21 labs, 2,220 participants
Obels et al. 2019	Psychology	Census	62 papers
Wayant et al 2019	Oncology	Census	154 meta-analyses
Simoneau et al. 2020	Bioinformatics	Robustness test	1 data set
Miyakawa 2020	Neurobiology	Census	41 papers
Thelwall et al 2020	Genetics	Census	1799 papers
Maassen et al 2020	Psychology	Reproduction	33 meta-analyses
Riedel et al 2020	Biomedical science	Census	792 papers
Culina et al 2020	Ecology	Census	346 papers
Clementi & Barba 2020	Physics	Replication	2 papers
Kemper et al 2020	Reproductive endocrinology	Census	222 papers
Marqués et al 2020	Biomedical sciences	Census	240 papers
Janssen et al 2020	Environmental Modelling	Census	7500 papers
Anderson et al 2020	Cardiology	Census	532 papers
Ostermann et al 2020	GIS	Census	75 papers
Samota & Davey 2020	Life sciences	Survey	251 researchers
Bedford & Tzovaras 2020	Genetics	Robustness test	1 paper
Krassowski et al 2020 (repo)	Life sciences	Census	3377 articles
Boudreau et al 2021	Computational Biology	Census	622 papers
Heumos et al 2021	Computational Biology	Robustness test	6 studies
Hrynaszkiewicz et al 2021	Computational Biology	Survey	214 researchers
Päll et al 2021	Differential expression	Census	2109 GEO submissions

Ad-hoc reproductions

These are one-off unpublished attempts to reproduce individual studies

Reproduction	Original study
https://rdoodles.rbind.io/2019/06/reanalyzing-data-from-human-gut-microbiota-from-autism-spectrum-disorder-promote-behavioral-symptoms-in-mice/ and https://notstatschat.rbind.io/2019/06/16/analysing-the-mouse-autism-data/	Sharon, G. et al. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. Cell 2019, 177 (6), 1600–1618.e17.
https://github.com/sean-harrison-bristol/CCR5_replication	Wei, X.; Nielsen, R. CCR5-∆32 Is Deleterious in the Homozygous State in Humans. Nat. Med. 2019 DOI: 10.1038/s41591-019-0459-6. (retracted)
https://github.com/leipzig/placenta	Leiby et al "Lack of detection of a human placenta microbiome in samples from preterm and term deliveries" https://doi.org/10.1186/s40168-018-0575-4

Theory papers

Authors/Date	Title	Field	Type
Ioannidis 2005	Why most published research findings are false	Science	Statistical reproducibility
Noble 2005	A Quick Guide to Organizing Computational Biology Projects	Bioinformatics	Best practices
Sandve et al 2013	Ten Simple Rules for Reproducible Computational Research	Computational science	Best practices
Freedman et al 2015	The Economics of Reproducibility in Preclinical Research	Preclinical research	Best practices
Yarkoni 2019	The Generalizability Crisis	Psychology	Statistical reproducibility
Bouthillier et al 2019	Unreproducible Research is Reproducible	Machine Learning	Methodology
Milton & Possolo 2019	Trustworthy data underpin reproducible research	Physics	Scientific philosophy
Devezer et al 2019	Scientific discovery in a model-centric framework: Reproducibility, innovation, and epistemic diversity	Science	Statistical reproducibility
Tierney et al 2020	A Realistic Guide to Making Data Available Alongside Code to Improve Reproducibility	Science	Best practices
Haibe-Kains et al 2020	The importance of transparency and reproducibility in artificial intelligence research	Artificial Intelligence	Critique
Nosek & Errington 2020	What is replication?	Science	Scientific philosophy
Alston & Rick 2020	A Beginner’s Guide to Conducting Reproducible Research	Ecology	Best Practices
Hejblum et al 2020	Realistic and Robust Reproducible Research for Biostatistics	Biostatistics	Best practices
Pawlik et al 2019	A Link is not Enough – Reproducibility of Data	Databases	Best practices
Schriml et al 2020	COVID-19 pandemic reveals the peril of ignoring metadata standards	Virology	Critique
Stoudt et al 2020	Principles for data analysis workflows	Data science	Best practices
Peng & Hicks 2020	Reproducible Research: A Retrospective	Public health	Review
Reiter et al 2020	Streamlining Data-Intensive Biology With Workflow Systems	Biology	Best practices
Ulrich & Miller 2020	Meta Research: Questionable research practices may have little effect on replicability	Science	Statistical reproducibility
Kasif & Roberts 2020	We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data	Functional genomics	Critique
Raman 2021	A research parasite's perspective on establishing a baseline to avoid errors in secondary analyses	Science	Best practices
Hoffmann et al 2021	The multiplicity of analysis strategies jeopardizes replicability: lessons learned across disciplines	Science	Critique

Tool reviews

Authors/Date	Title	Tools
Isdahl & Gundersen 2019	Out-of-the-box Reproducibility: A Survey of Machine Learning Platforms	MLflow, Polyaxon, StudioML, Kubeflow, CometML, Sagemaker, GCPML, AzureML, Floydhub, BEAT, Codalab, Kaggle
Pimentel et al 2019	A Survey on Collecting, Managing, and Analyzing Provenance from Scripts	Astro-Wise, CPL, CXXR, Datatrack, ES3, ESSW, IncPy, Lancet, Magni, noWorkflow, Provenance Curios, pypet, RDataTracker, Sacred, SisGExp, SPADE, StarFlow, Sumatra, Variolite, VCR, versuchung, WISE, YesWorkflow
Leipzig et al 2019 (supplemental)	The Role of Metadata in Reproducible Computational Research	CellML, CIF2, DATS, DICOM, EML, FAANG, GBIF, GO, ISO/TC 276, MIAME, NetCDF, OGC, ThermoML, CRAN, Conda, pip setup.cfg, EDAM, CodeMeta, Biotoolsxsd, DOAP, ontosoft, SWO, OBCS, STATO, SDMX, DDI, MEX, MLSchema, MLFlow, Rmd, CWL, CWLProv, RO-Crate, RO, WICUS, OPM, PROV-O, ReproZip, ProvOne, WES, BagIt, BCO, ERC, BEL, DC, JATS, ONIX, MeSH, LCSH, MP, Open PHACTS, SWAN, SPAR, PWO, PAV, Manubot, ReScience, PandocScholar
Konkol, Markus, Nüst, Daniel, Goulier, Laura 2020	Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication	Authorea, Binder, CodeOcean, eLife RDS, Galaxy Project, Gigantum, Manuscript, o2r, REANA, ReproZip, Whole tale

Courses

• MOOCs
  • 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.
• Online course content
  • Tools for Reproducible Research - Karl Broman UW, includes resources page
  • R for Reproducible Scientific Analysis - Software Carpentry workshop primer using Gapminder data
  • R-DAVIS - Student-developed computer literacy and data course in R
  • AMIA2019 - Pragmatic RR for Analysis, Dissemination and Publication
  • PSU-PSY525 - Transparent, Open, and Reproducible Research Practices in the Social and Behavioral Sciences
  • Monash-RRR - Reproducible Research in R workshop tutorial
  • OSU-OSRR - An open science and reproducible research course targeted at organismal ecologists

Development Resources

• R
  • CRAN Task View - Reproducible Research - packages relevant to RCR in R
  • liftr - persistent reproducible reporting through containerized R Markdown documents
  • repo - provenance framework package
  • orderly - R package that automates writing reproducible analyses
• Python
  • mlf-core - Framework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost

User tools

• Open With Binder for Chrome or Firefox - open the GitHub repository you are visiting using MyBinder.org
• DVC - DVC tracks machine learning models and data sets
• 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.

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
• The Turing Way: A Handbook for Reproducible Data Science 2020
• Reproducibility and Replicability in Science
• Reproducibility: Principles, Problems, Practices, and Prospects

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

Data Repositories

All these repositories assign Digital Object Identifiers (DOIs) to data

• DataCite - 12M+ DOIs registered for 46 allocators. Offers APIs and a metadata schema.
• 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
• OSF - Project-oriented system with access control and integration with popular tools. Unlimited storage for projects, but individual files are limited to 5 gigabytes (GB) each.
• Zenodo - Allows embargoed, restricted access, metadata support. 50GB limit.

Exemplar Portals

Places to find papers with code or portals to host them

• Jupyter Gallery - Gallery of interesting Jupyter notebooks
• Papers With Code - ML papers with code
• NARPS - Code related to Neuroimaging Analysis Replication and Prediction Study
• Codeocean - A gallery of cloud-based containers with reproducible analyses

Runnable Papers

Experimental papers that have associated notebooks

Haibe-Kains lab

Publication	CodeOcean link
Mer AS et al. Integrative Pharmacogenomics Analysis of Patient Derived Xenografts	codeocean.com/capsule/056639
Gendoo, Zon et al. MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature	codeocean.com/capsule/643863
Yao et al. Tissue specificity of in vitro drug sensitivity	codeocean.com/capsule/550275
Safikhani Z et al. Gene isoforms as expression-based biomarkers predictive of drug response in vitro	codeocean.com/capsule/000290
El-Hachem et al. Integrative cancer pharmacogenomics to infer large-scale drug taxonomy	codeocean.com/capsule/425224
Safikhani Z et al. Revisiting inconsistency in large pharmacogenomic studies	codeocean.com/capsule/627606
Sandhu V et al. Meta-analysis of 1,200 transcriptomic profiles identifies a prognostic model for pancreatic ductal adenocarcinoma	codeocean.com/capsule/269362

Patcher lab

Publication	Github link
Pimental et al 2017. Differential analysis of RNA-seq incorporating quantification uncertainty	sleuth_paper_analysis
Melsted et al 2019. Modular and efficient pre-processing of single-cell RNA-seq	MBGBLHGP_2019
Chari et al 2021. Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types	CWGFLHGCCHAP_2021

Siepel lab

Blumberg et al 2021. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

https://codeocean.com/capsule/7351682

Journals

• ReScience - Journal dedicated to insilico reproductions and tests of robustness, lives on Github.
• eLife - Executable Research Articles (ERA) inline executable blocks

Ontologies

• FAIRsharing - standards, databases, and policies
• BioPortal - 660 biomedical ontologies

Minimal Standards

• STORMS - Strengthening The Organization and Reporting of Microbiome Studies (STORMS) is a checklist for reporting on human microbiome studies. Preprint

Organizations

• ResearchObject.org - RO specifications and publications
• BioCompute - BCO specs
• rOpenSci - Tools, conferences, and education
• Open Science Framework - Open source project management
• 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
• 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.

Awesome Lists

• 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 Jupyter - Jupyter projects, libraries and resources
• Awesome Bioinformatics Benchmarks - Benchmarks are a related aspect of robustness testing
• Awesome Open Science - Resources, data, tools, and scholarship
• Awesome Public Datasets - A topic-centric list of HQ open datasets
• Awesome Semantic Web - Semantic web and linked data resources.

Contribute

Contributions welcome! Read the contribution guidelines first. You may find my src/doi2md.py script useful for quickly generating entries from a DOI.

License

To the extent possible under law, Jeremy Leipzig has waived all copyright and related or neighboring rights to this work.