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
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Linked from 2 awesome lists

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Awesome Reproducible Research / Case studies

Awesome Reproducible Research / 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

Awesome Reproducible Research / Courses / 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 4 3 months ago Pragmatic RR for Analysis, Dissemination and Publication
PSU-PSY525 3 10 months ago Transparent, Open, and Reproducible Research Practices in the Social and Behavioral Sciences
Monash-RRR Reproducible Research in R workshop tutorial
OSU-OSRR 57 over 5 years ago An open science and reproducible research course targeted at organismal ecologists
Reproducible-Science-Curriculum A curriculum for teaching reproducible computational science bootcamps

Awesome Reproducible Research / Development Resources / R
CRAN Task View - Reproducible Research packages relevant to RCR in R
liftr persistent reproducible reporting through containerized R Markdown documents
repo 20 over 3 years ago provenance framework package
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

Awesome Reproducible Research / Development Resources / Python
mlf-core Framework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost

Awesome Reproducible Research / Literature tools
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
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

Awesome Reproducible Research / Scientific Data Management Systems
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
Fairly Toolset Tools 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 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

Awesome Reproducible Research / 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

Awesome Reproducible Research / Data Repositories
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

Awesome Reproducible Research / Exemplar Portals
Jupyter Gallery 14,937 25 days ago Gallery of interesting Jupyter notebooks
Papers With Code ML papers with code
NARPS 34 over 4 years ago Code related to Neuroimaging Analysis Replication and Prediction Study
Codeocean A 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_analysis 16 about 6 years ago
Melsted et al 2019. Modular and efficient pre-processing of single-cell RNA-seq
MBGBLHGP_2019 23 almost 4 years ago
Chari et al 2021. Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity of Clytia Medusa Cell Types
CWGFLHGCCHAP_2021 2 9 months 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
ReScience Journal dedicated to insilico reproductions and tests of robustness, lives on Github
eLife Executable Research Articles (ERA) inline executable blocks

Awesome Reproducible Research / Ontologies
FAIRsharing standards, databases, and policies
BioPortal 660 biomedical ontologies

Awesome Reproducible Research / Minimal Standards
STORMS Strengthening The Organization and Reporting of Microbiome Studies (STORMS) is a checklist for reporting on human microbiome studies

Awesome Reproducible Research / 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
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
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 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

Awesome Reproducible Research / Awesome Lists
Awesome Pipeline 6,204 about 1 month ago So many pipelines frameworks
Awesome Docker 30,488 9 days ago Everything related to the Docker containerization system
Awesome R 6,024 6 months ago Section on RR tools
Awesome Reproducible R 13 about 1 year ago RRR tools
Awesome Jupyter 4,047 1 day ago Jupyter projects, libraries and resources
Awesome Bioinformatics Benchmarks 315 3 months ago Benchmarks are a related aspect of robustness testing
Awesome Open Science 43 about 1 year ago Resources, data, tools, and scholarship
Awesome Public Datasets 60,953 8 days ago A topic-centric list of HQ open datasets
Awesome Semantic Web 1,422 about 2 months ago Semantic web and linked data resources

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