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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 18 hours ago
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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

  • Courses

  • 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

  • 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.

  • Books

  • 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

  • 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.
    • Figshare - 20 GB of free private space, unlimited public space, >2M articles, >5k projects

  • Organizations

    • 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

  • Exemplar Portals

  • Journals

    • Siepel lab

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

  • Ontologies

  • Minimal Standards

    • 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)

  • Awesome Lists

Programming Languages
R 1
Categories
Organizations 14 Books 7 Courses 6 Development Resources 6 Data Repositories 4 Scientific Data Management Systems 4 Awesome Lists 3 Exemplar Portals 3 Databases 3 Ontologies 2 Journals 2 Literature tools 2 License 2 Minimal Standards 1
Sub Categories
Siepel lab 24
Keywords
awesome 2 awesome-list 2 list 2 container 1 docker 1 docker-api 1 docker-container 1 docker-deployment 1 docker-environment 1 docker-image 1 docker-machine 1 docker-monitoring 1 docker-registry 1 docker-security 1 docker-swarm 1 dockerfile 1 moby 1 tools 1 data-analysis 1 data-science 1 r 1 rstats 1 aaron-swartz 1 awesome-public-datasets 1 datasets 1 opendata 1