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

Singularity: Application containers for Linux

A DSL for data-driven computational pipelines

rrtools: Tools for Writing Reproducible Research in R

Workflow Description Language - Specification and Implementations

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

Containerize R Markdown documents for continuous reproducibility

RNA-seq workflow using STAR and DESeq2

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.

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).

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

High performance spatial analysis in a Web Browser or Node.js

Future Gadget Machine

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

🔬 Empirical CLI

List of Reproducible Audio Research Papers

unit-testing for a collection of jupyter notebooks using nbconvert

SEER, reimplemented in python 🐍🔮

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Source code for the CERN Analysis Preservation portal

Reproducible Science: what, why, how

Electromagnetic methods in geophysics - open educational resources.

Project directory generator R package

A presentation on best coding/data management practices based on my own experiences of scientific computing and data analysis and heavily borrowing from the recommendations of many others. View presentation at: https://edeno.github.io/Better-Science-Code

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