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reproducible-science

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IDSIA /sacred

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

python infrastructure machine-learning mongodb reproducible-research reproducible-science reproducibility

UpdatedOct 22, 2025
Python

nextflow

nextflow-io /nextflow

A DSL for data-driven computational pipelines

docker groovy hello aws cloud bioinformatics pipeline nextflow hpc reproducible-research workflow-engine slurm pipeline-framework sge singularity reproducible-science dataflow singularity-containers

UpdatedDec 17, 2025
Groovy

apptainer /singularity

Singularity has been renamed to Apptainer as part of us moving the project to the Linux Foundation. This repo has been persisted as a snapshot right before the changes.

linux science hpc reproducible portable containers parallel container singularity reproducible-science cloud-native singularity-container portability rootless-containers

UpdatedOct 10, 2022
Go

openwdl /wdl

Specification for the Workflow Description Language (WDL).

workflow cloud bioinformatics reproducible-science wdl reproducibility openwdl

UpdatedNov 10, 2025

benmarwick /rrtools

rrtools: Tools for Writing Reproducible Research in R

r reproducible-research reproducible-science research-tool research-project reproducibility research-paper quarto reproducible-paper research-compendium quarto-template

UpdatedJul 21, 2025
R

showyourwork /showyourwork

A workflow for reproducible and open scientific articles

open-source latex continuous-integration reproducible-research reproducible-science scientific-workflows scientific-papers

UpdatedDec 15, 2025
TeX

mit-ll-responsible-ai /hydra-zen

Create powerful Hydra applications without the yaml files and boilerplate code.

machine-learning scalable deep-learning configuration pytorch reproducible-science machinelearning configurable reproducibility yaml-configuration dynamic-configuration dataclasses pytorch-lightning

UpdatedDec 15, 2025
Python

awesome-reproducible-research

leipzig /awesome-reproducible-research

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

awesome reproducible-research reproducible-science awesome-list reproducibility reproducible-workflows reproducible-analysis

UpdatedDec 14, 2025
Python

reprozip

VIDA-NYU /reprozip

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

python linux docker science vagrant reproducible-research archiving reproducible-science scientific-computing ptrace reproducibility computational-science reprozip reprounzip hacktoberfest nyu

UpdatedDec 8, 2025
Python

genecell /single-cell-papers-with-code

Papers with code for single cell related papers

reproducible-research reproducible-science scrna-seq single-cell single-cell-rna-seq single-cell-atac-seq single-cell-omics scrna-seq-analysis paper-with-code

UpdatedJul 14, 2023

containerit

o2r-project /containerit

Package an R workspace and all dependencies as a Docker container

docker dockerfile r reproducible-research reproducible-science

UpdatedFeb 17, 2022
R

Kaixhin /FGLab

Future Gadget Laboratory

machine-learning reproducible-research reproducible-science

UpdatedMar 3, 2018
HTML

InsightSoftwareConsortium /ITK-Wasm

High performance spatial analysis in a web browser and across programming languages and hardware architectures

visualization javascript webassembly wasm emscripten open-science reproducible-science itk imaging insight-toolkit input-output wasi itk-module

UpdatedDec 8, 2025
Python

shournal

tycho-kirchner /shournal

Log shell-commands and used files. Snapshot executed scripts. Fully automatic.

shell bash zsh reproducible-research provenance reproducible-science reproducibility computational-science lowlevel command-tracker file-tracker

UpdatedApr 10, 2025
C++

nanxstats /liftr

🐳 Containerize R Markdown documents for continuous reproducibility

docker reproducible-research rmarkdown reproducible-science knitr dynamic-documents containerization statistical-computing liftr

UpdatedMar 11, 2024
R

alan-turing-institute /TCPDBench

The Turing Change Point Detection Benchmark: An Extensive Benchmark Evaluation of Change Point Detection Algorithms on real-world data

benchmark reproducible-research reproducible-science benchmark-suite changepoint change-detection change-point reproducible-paper change-point-detection

UpdatedJul 31, 2025

Sarek

SciLifeLab /Sarek

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

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity reproducible-science somatic germline germline-variants

UpdatedJan 27, 2020
Nextflow

mgalardini /pyseer

SEER, reimplemented in python 🐍🔮

gwas reproducible-science reimplementation bacteria k-mer

UpdatedMay 22, 2025
Python

everware /everware

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

docker reproducible-research jupyter-notebook reproducible-science

UpdatedJun 23, 2018
Python

deanmarchiori /analysis-flow

Data Analysis Workflows & Reproducibility Learning Resources

workflow tooling reproducible-science data-analysis reproducibility reproducible-data-science

UpdatedMar 4, 2021

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