awesome-reproducible-research

Roger Peng et al JHU. Very popular course

John Quackenbush et al Harvard

Beginner level. Note taking, version control, notebooks, reproducible data analysis. Bilingual English/French

Karl Broman UW, includes resources page

Software Carpentry workshop primer using Gapminder data

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

Reproducible Research in R workshop tutorial

OSU-OSRR

An open science and reproducible research course targeted at organismal ecologists

A curriculum for teaching reproducible computational science bootcamps

packages relevant to RCR in R

persistent reproducible reporting through containerized R Markdown documents

repo

provenance framework package

R package that automates writing reproducible analyses

a set of software development practices that create an independently-verifiable path from source to binary code

Framework to develop GPU deterministic machine learning models with PyTorch, TensorFlow and XGBoost

Citation statement AI for discovering and evaluating scientific articles

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 quickly scans research manuscripts or articles to identify and record key reproducibility variables, such as data availability, code acknowledgements, and research analysis methods

DVC tracks machine learning models and data sets

Git-based versioning for data and provenance

Portal, query interface, visualization and schema framework that powers ICGC, KFDC, GDC

Tools for preparing, publishing and downloading datasets from research data repositories directly into computing environments. It provides integration with and

Describes projects: Sumatra, Vistrails, CDE, SOLE, JUMBO, CML, knitr. Content available on OSF

31 first person case narratives and intro chapters

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

1211 replication findings on 333 psychology studies

12M+ DOIs registered for 46 allocators. Offers APIs and a metadata schema

curated, metadata-centric, focused on articles associated with published artices, $120 submission fee (various waivers available)

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

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

Allows embargoed, restricted access, metadata support. 50GB limit

Jupyter Gallery

Gallery of interesting Jupyter notebooks

ML papers with code

NARPS

Code related to Neuroimaging Analysis Replication and Prediction Study

A gallery of cloud-based containers with reproducible analyses

Journal dedicated to insilico reproductions and tests of robustness, lives on Github

Executable Research Articles (ERA) inline executable blocks

standards, databases, and policies

660 biomedical ontologies

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

RO specifications and publications

BCO specs

Tools, conferences, and education

Open source project management

Promotes open and reproducible research through peer-review of scientific Python packages

Furthering the practice of replication in economics. Econ replication database

Estimating the replicability of research in the social sciences

1-day reproducibility hackathons held worldwide

community for checking executability of scientific preprints and papers

Certification Agency for Scientific Code and Data. Issues reproducibility certificates

Community-led reproducibility workshops

curation of research and code for digital preservation

manuscripts & presentations

transparency and quality of marketing research published in academic journals

online platform designed to collect and share information on the provenance and availability of the data for all articles co-authored by Francesca Gino

Framework for Open and Reproducible Research Training advancing research transparency, reproducibility, rigor, and ethics through pedagogical reform and meta-scientific research

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