Top 35 reproducible-science open source projects

Package an R workspace and all dependencies as a Docker container

ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

Future Gadget Laboratory

Singularity: Application containers for Linux

RNA-seq workflow using STAR and DESeq2

🐳 Containerize R Markdown documents for continuous reproducibility

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Everware is about re-useable science, it allows people to jump right in to your research code.

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

A DSL for data-driven computational pipelines

VisTrails is an open-source data analysis and visualization tool. It provides a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the computational processes that derive these products and their executions.

dcmjs is a javascript cross-compile of dcmtk (dcmtk.org).

SEER, reimplemented in python 🐍🔮

Source code for the CERN Analysis Preservation portal

rrtools: Tools for Writing Reproducible Research in R

Workflow Description Language - Specification and Implementations

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

Future Gadget Machine

Software Papers as Software Modules: Towards a Culture of Reusable Results

Open Source Photometric classification https://supernnova.readthedocs.io

Examples and demos for ReproZip

Reproducible Data Science in Python (SciPy 2019 Tutorial)

🔬 Empirical CLI

Papers with code for single cell related papers

NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

Short course on reproducible science: what, why, how

Reproducible Science: what, why, how

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!

Fully reproducible, open source scientific articles in LaTeX.

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

Data Analysis Workflows & Reproducibility Learning Resources

Pythonic functions for creating and enhancing Hydra applications

Seamless is a framework to set up reproducible computations (and visualizations) that respond to changes in cells. Cells contain the input data as well as the source code of the computations, and all cells can be edited interactively.