awesome-reproducible-research

Research guides

A curated list of resources and case studies promoting transparent and reproducible research practices in various fields.

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

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Language: Python
last commit: almost 2 years ago
Linked from 2 awesome lists

awesomeawesome-listreproducibilityreproducible-analysisreproducible-researchreproducible-sciencereproducible-workflows

Awesome Reproducible Research / Case studies

Awesome Reproducible Research / Courses / MOOCs

Coursera Reproducible ResearchRoger Peng et al JHU. Very popular course
edX Principles, Statistical and Computational Tools for Reproducible ScienceJohn Quackenbush et al Harvard
Reproducible research: methodological principles for transparent scienceBeginner level. Note taking, version control, notebooks, reproducible data analysis. Bilingual English/French

Awesome Reproducible Research / Courses / Online course content

Tools for Reproducible ResearchKarl Broman UW, includes resources page
R for Reproducible Scientific AnalysisSoftware Carpentry workshop primer using Gapminder data
R-DAVISStudent-developed computer literacy and data course in R
AMIA20194about 2 years agoPragmatic RR for Analysis, Dissemination and Publication
PSU-PSY5253over 2 years agoTransparent, Open, and Reproducible Research Practices in the Social and Behavioral Sciences
Monash-RRRReproducible Research in R workshop tutorial
OSU-OSRR57over 7 years agoAn open science and reproducible research course targeted at organismal ecologists
Reproducible-Science-CurriculumA curriculum for teaching reproducible computational science bootcamps

Awesome Reproducible Research / Development Resources / R

CRAN Task View - Reproducible Researchpackages relevant to RCR in R
liftrpersistent reproducible reporting through containerized R Markdown documents
repo20over 5 years agoprovenance framework package
orderlyR package that automates writing reproducible analyses
Reproducible Buildsa set of software development practices that create an independently-verifiable path from source to binary code

Awesome Reproducible Research / Development Resources / Python

mlf-coreFramework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost

Awesome Reproducible Research / Literature tools

SciteCitation statement AI for discovering and evaluating scientific articles
SciScoreSciScore 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
RipetaRipeta quickly scans research manuscripts or articles to identify and record key reproducibility variables, such as data availability, code acknowledgements, and research analysis methods

Awesome Reproducible Research / Scientific Data Management Systems

DVCDVC tracks machine learning models and data sets
DataLadGit-based versioning for data and provenance
OverturePortal, query interface, visualization and schema framework that powers ICGC, KFDC, GDC
Fairly ToolsetTools for preparing, publishing and downloading datasets from research data repositories directly into computing environments. It provides integration with and

Awesome Reproducible Research / Books

Reproducible Research with R and R Studio 2013
Implementing Reproducible Research 2014Describes projects: Sumatra, Vistrails, CDE, SOLE, JUMBO, CML, knitr. Content available on OSF
The Practice of Reproducible Research 201731 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

Awesome Reproducible Research / Databases

ReplicationWikiDatabase 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
ReplicationDatabase1211 replication findings on 333 psychology studies

Awesome Reproducible Research / Data Repositories

DataCite12M+ DOIs registered for 46 allocators. Offers APIs and a metadata schema
Data Dryadcurated, metadata-centric, focused on articles associated with published artices, $120 submission fee (various waivers available)
Figshare20 GB of free private space, unlimited public space, >2M articles, >5k projects
OSFProject-oriented system with access control and integration with popular tools. Unlimited storage for projects, but individual files are limited to 5 gigabytes (GB) each
ZenodoAllows embargoed, restricted access, metadata support. 50GB limit

Awesome Reproducible Research / Exemplar Portals

Jupyter Gallery14,964almost 2 years agoGallery of interesting Jupyter notebooks
Papers With CodeML papers with code
NARPS34over 6 years agoCode related to Neuroimaging Analysis Replication and Prediction Study
CodeoceanA gallery of cloud-based containers with reproducible analyses

Awesome Reproducible Research / Runnable Papers / Haibe-Kains lab

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
Sharifi-Noghabi et al Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models
codeocean.com/capsule/7358839
Arrowsmith et al Automated detection of dental artifacts for large-scale radiomic analysis in radiation oncology
codeocean.com/capsule/2097894
Mer et al Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
codeocean.com/capsule/8791617
Ortmann et al KuLGaP: A Selective Measure for Assessing Therapy Response in Patient-Derived Xenografts
codeocean.com/capsule/2817911
Madani Tonekaboni et al Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations
codeocean.com/capsule/6911149
Seo et al SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology
codeocean.com/capsule/6322807
Mammoliti et al Creating reproducible pharmacogenomic analysis pipelines
codeocean.com/capsule/6718332
Manem et al Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy
codeocean.com/capsule/1166221
Tonekaboni et al CREAM: Clustering of genomic REgions Analysis Method
codeocean.com/capsule/0002901
Madani Tonekaboni et al SIGN: similarity identification in gene expression
codeocean.com/capsule/0544852
Mer et al Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts
codeocean.com/capsule/0566399
Sandhu et al Applications of Computational Systems Biology in Cancer Signaling Pathways
codeocean.com/capsule/0795540
Sandhu et al Meta-Analysis of 1,200 Transcriptomic Profiles Identifies a Prognostic Model for Pancreatic Ductal Adenocarcinoma
codeocean.com/capsule/7402260
Gendoo et al MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature
codeocean.com/capsule/6438633
Yao et al Tissue specificity of in vitro drug sensitivity
codeocean.com/capsule/5502756
Safikhani et al Gene isoforms as expression-based biomarkers predictive of drug response in vitro
codeocean.com/capsule/0002901
El-Hachem et al Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy
codeocean.com/capsule/4252248
Safikhani et al Revisiting inconsistency in large pharmacogenomic studies
codeocean.com/capsule/6276064

Awesome Reproducible Research / Runnable Papers / Patcher lab

Pimental et al 2017. Differential analysis of RNA-seq incorporating quantification uncertainty
sleuth_paper_analysis16almost 8 years ago
Melsted et al 2019. Modular and efficient pre-processing of single-cell RNA-seq
MBGBLHGP_201923over 5 years ago
Chari et al 2021. Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types
CWGFLHGCCHAP_20212over 2 years ago

Awesome Reproducible Research / Runnable Papers / 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

Awesome Reproducible Research / Journals

ReScienceJournal dedicated to insilico reproductions and tests of robustness, lives on Github
eLifeExecutable Research Articles (ERA) inline executable blocks

Awesome Reproducible Research / Ontologies

FAIRsharingstandards, databases, and policies
BioPortal660 biomedical ontologies

Awesome Reproducible Research / Minimal Standards

STORMSStrengthening The Organization and Reporting of Microbiome Studies (STORMS) is a checklist for reporting on human microbiome studies

Awesome Reproducible Research / Organizations

ResearchObject.orgRO specifications and publications
BioComputeBCO specs
rOpenSciTools, conferences, and education
Open Science FrameworkOpen source project management
pyOpenSciPromotes open and reproducible research through peer-review of scientific Python packages
Replication NetworkFurthering the practice of replication in economics. Econ replication database
repliCATS projectEstimating the replicability of research in the social sciences
ReproHack1-day reproducibility hackathons held worldwide
CODECHECKcommunity for checking executability of scientific preprints and papers
CASCaDCertification Agency for Scientific Code and Data. Issues reproducibility certificates
Reproducibility for EveryoneCommunity-led reproducibility workshops
CUrating for REproducibilitycuration of research and code for digital preservation
Michigan Institute for Data Science Reproducibility Hubmanuscripts & presentations
OpenMKTtransparency and quality of marketing research published in academic journals
Many Co-Authorsonline platform designed to collect and share information on the provenance and availability of the data for all articles co-authored by Francesca Gino
FORRTFramework for Open and Reproducible Research Training advancing research transparency, reproducibility, rigor, and ethics through pedagogical reform and meta-scientific research

Awesome Reproducible Research / Awesome Lists

Awesome Pipeline6,227almost 2 years agoSo many pipelines frameworks
Awesome Docker30,735almost 2 years agoEverything related to the Docker containerization system
Awesome R6,047almost 2 years agoSection on RR tools
Awesome Reproducible R13almost 3 years agoRRR tools
Awesome Jupyter4,083almost 2 years agoJupyter projects, libraries and resources
Awesome Bioinformatics Benchmarks318about 2 years agoBenchmarks are a related aspect of robustness testing
Awesome Open Science44about 3 years agoResources, data, tools, and scholarship
Awesome Public Datasets61,377almost 2 years agoA topic-centric list of HQ open datasets
Awesome Semantic Web1,433almost 2 years agoSemantic web and linked data resources

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