GitHub topics: reproducibility

Repositories

Elisseeff-Lab/etbf_fbr_stromal_bulkseq

Bulk RNAseq analysis of stromal cells from peri-implant fibrosis of mice with and without ETBF infection

Language: R - Size: 6.41 MB - Last synced at: about 4 hours ago - Pushed at: about 5 hours ago - Stars: 0 - Forks: 0

sandialabs/staged-script

A Python package enabling the development of robust automation scripts that are subdivided into stages.

Language: Python - Size: 581 KB - Last synced at: about 4 hours ago - Pushed at: about 5 hours ago - Stars: 21 - Forks: 1

sandialabs/shell-logger

A Python package that allows you to interact with the shell, while logging various metadata, statistics, and trace information.

Language: Python - Size: 1.54 MB - Last synced at: about 4 hours ago - Pushed at: about 6 hours ago - Stars: 2 - Forks: 1

iterative/dvc

🦉 Data Versioning and ML Experiments

Language: Python - Size: 19.5 MB - Last synced at: about 5 hours ago - Pushed at: about 9 hours ago - Stars: 14,444 - Forks: 1,210

Kirito7111/stepup-queue

Integrates queued jobs into a StepUp workflow.

Language: Python - Size: 38.1 KB - Last synced at: about 8 hours ago - Pushed at: about 8 hours ago - Stars: 0 - Forks: 0

wandb/wandb

The AI developer platform. Use Weights & Biases to train and fine-tune models, and manage models from experimentation to production.

Language: Python - Size: 172 MB - Last synced at: about 11 hours ago - Pushed at: about 22 hours ago - Stars: 9,852 - Forks: 739

oliverweissl/CondaDependencyCleaner

Streamline your Conda environments by pruning unnecessary transitive dependencies, build strings, and version constraints from .yml files. Enjoy faster installs, clearer setups, and dependable reproducibility

Language: Python - Size: 72.3 KB - Last synced at: about 16 hours ago - Pushed at: about 16 hours ago - Stars: 1 - Forks: 0

the-nix-way/dev-templates

Dev environments for numerous languages based on Nix flakes [maintainer=@lucperkins]

Language: Nix - Size: 434 KB - Last synced at: about 15 hours ago - Pushed at: about 17 hours ago - Stars: 1,630 - Forks: 133

LinguaPhylo/linguaPhylo

LinguaPhylo: A language for describing, visualising and simulating probabilistic phylogenetic models

Language: Java - Size: 127 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 22 - Forks: 8

reproducible-reporting/stepup-queue

Integrates queued jobs into a StepUp workflow.

Language: Python - Size: 30.3 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0

reproducible-reporting/stepup-reprep

StepUp RepRep is the StepUp extension for Reproducible Reporting

Language: Python - Size: 2.49 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 3 - Forks: 3

DavHau/mach-nix

Create highly reproducible python environments

Language: Python - Size: 663 KB - Last synced at: 1 day ago - Pushed at: 12 months ago - Stars: 884 - Forks: 107

reproducible-reporting/stepup-core

A simple, powerful and universal build tool

Language: Python - Size: 7.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 4 - Forks: 2

stal-ix/ix

ix package manager, statically build packages, for darwin/linux, with clang

Language: Shell - Size: 27.5 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 143 - Forks: 16

biosimulations/biosimulations

A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results

Language: TypeScript - Size: 198 MB - Last synced at: about 14 hours ago - Pushed at: 2 days ago - Stars: 41 - Forks: 14

solislemuslab/solislemuslab.github.io

Github repo for SolisLemus lab website

Language: TeX - Size: 136 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 1 - Forks: 33

open-science-community-uppsala/open_science_community_uppsala

The Open Science community in Uppsala

Language: Shell - Size: 304 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 6 - Forks: 0

shunichironomura/capsula

A Python package to record function execution contexts for reproducibility

Language: Python - Size: 4.08 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2 - Forks: 0

VolodiaPG/nixos-configs

NixOS configuraitons for my machines

Language: Nix - Size: 51.8 MB - Last synced at: 2 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 0

zincware/ZnTrack

Create, visualize, run & benchmark DVC pipelines in Python & Jupyter notebooks.

Language: Python - Size: 9.33 MB - Last synced at: about 6 hours ago - Pushed at: about 8 hours ago - Stars: 52 - Forks: 5

mahermanns/jube-novice

An introductory lesson on using JUBE for HPC workloads.

Language: TeX - Size: 15.2 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

rlworkgroup/garage

A toolkit for reproducible reinforcement learning research.

Language: Python - Size: 57.6 MB - Last synced at: about 21 hours ago - Pushed at: about 2 years ago - Stars: 1,973 - Forks: 315

EX539/docker-dev-env

A collection of ready-to-use Docker development environments for multiple Linux distributions (Ubuntu, Debian, Alpine, Arch, Kali). Includes shared configurations, utility scripts, and comprehensive documentation for reproducible development setups across teams and CI/CD pipelines.

Language: Shell - Size: 14.6 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

SwissDataScienceCenter/renku

Renku provides a platform and tools for reproducible and collaborative data analysis.

Language: Scala - Size: 37.5 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 238 - Forks: 33

the-Hull/datacleanr

Interactive and Reproducible Data Cleaning

Language: R - Size: 24.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 21 - Forks: 5

kletobias/advanced-mlops-lifecycle-hydra-mlflow-optuna-dvc

End-to-end MLOps pipeline showcasing senior-level best practices with Hydra for configuration, MLflow for experiment tracking, Optuna for hyperparameter tuning, and DVC for data/version control. This repository focuses on reproducibility, modular design, and streamlined collaboration—an ideal demonstration of advanced MLOps capabilities.

Language: Python - Size: 960 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 1 - Forks: 0

glotzerlab/signac

Manage large and heterogeneous data spaces on the file system.

Language: Python - Size: 7.2 MB - Last synced at: 4 days ago - Pushed at: 5 days ago - Stars: 132 - Forks: 37

ReproducibiliTea-org/reproducibiliTea

Website for the ReproducibiliTea Journal Club and Podcast

Language: HTML - Size: 6.81 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 8 - Forks: 26

sandialabs/reverse_argparse

A Python library to determine what exactly the user ran at the command line, along with default values, and any transformations that happened after parsing arguments.

Language: Python - Size: 663 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 41 - Forks: 5

ropensci/rix

Reproducible Data Science environments for R with Nix

Language: R - Size: 14.6 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 249 - Forks: 17

catalyst-team/catalyst

Accelerated deep learning R&D

Language: Python - Size: 52.6 MB - Last synced at: 5 days ago - Pushed at: about 1 year ago - Stars: 3,350 - Forks: 393

LibraryCarpentry/lc-reproducible-research

Introduction to reproducible research concepts and tools for librarians.

Size: 8.18 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

emacs-twist/twist.nix

Build an entire Emacs configuration as a Nix package in a pure, reproducible way

Language: Nix - Size: 475 KB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 93 - Forks: 10

calkit/calkit

A framework and toolkit for analytical/research projects, with an emphasis on reproducibility.

Language: Python - Size: 8.67 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 20 - Forks: 0

IDSIA/sacred

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

Language: Python - Size: 5.87 MB - Last synced at: 5 days ago - Pushed at: 6 months ago - Stars: 4,297 - Forks: 382

mlr-org/batchtools

Tools for computation on batch systems

Language: R - Size: 4.15 MB - Last synced at: 6 days ago - Pushed at: over 1 year ago - Stars: 179 - Forks: 51

ddsjoberg/gtsummary

Presentation-Ready Data Summary and Analytic Result Tables

Language: R - Size: 690 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,109 - Forks: 133

ledwindra/replication-code-economics

Track publicly available replication codes/supplemental materials in economics (currently top 10) journals

Language: Jupyter Notebook - Size: 34.9 MB - Last synced at: 3 days ago - Pushed at: 6 days ago - Stars: 18 - Forks: 10

snakemake/snakemake

This is the development home of the workflow management system Snakemake. For general information, see

Language: Python - Size: 89.6 MB - Last synced at: 6 days ago - Pushed at: 13 days ago - Stars: 2,467 - Forks: 592

understandable-machine-intelligence-lab/Quantus

Quantus is an eXplainable AI toolkit for responsible evaluation of neural network explanations

Language: Jupyter Notebook - Size: 147 MB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 598 - Forks: 77

ropensci/targets

Function-oriented Make-like declarative workflows for R

Language: R - Size: 6.91 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 994 - Forks: 75

cthoyt/autoreviewer

👁️‍🗨️ Scientists often do the same bad stuff. Automate giving feedback during peer review.

Language: Python - Size: 444 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 26 - Forks: 0

catalyst-cooperative/pudl-archiver

A tool for capuring snapshots of public data sources and archiving them on Zenodo for programmatic use.

Language: Python - Size: 2.42 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 14 - Forks: 6

ropensci/geotargets

Targets extensions for geospatial data

Language: R - Size: 3.65 MB - Last synced at: 6 days ago - Pushed at: 8 days ago - Stars: 80 - Forks: 5

carpentries-incubator/reproducible-research-through-reusable-code-in-1-day

Lesson material for Reproducible research through reusable code workshop

Size: 8.77 MB - Last synced at: about 1 hour ago - Pushed at: about 2 hours ago - Stars: 2 - Forks: 2

lnnrtwttkhn/repro-book

Source code for the Repro Book, an online guide to reproducible research

Language: R - Size: 8.34 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 1

maxhbr/myconfig

my Linux Configuration

Language: Shell - Size: 426 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 38 - Forks: 12

forrtproject/forrtproject.github.io

FORRT Website

Language: HTML - Size: 515 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 35 - Forks: 22

HALFpipe/HALFpipe

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

Language: Python - Size: 9.17 MB - Last synced at: 3 days ago - Pushed at: 7 days ago - Stars: 92 - Forks: 14

nix-community/dream2nix

Simplified nix packaging for various programming language ecosystems [maintainer=@DavHau]

Language: Nix - Size: 26 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1,119 - Forks: 139

ropensci/tarchetypes

Archetypes for targets and pipelines

Language: R - Size: 2.04 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 144 - Forks: 21

opengisci/opengisci.github.io

Open Geographic Information Science Curriculum

Language: HTML - Size: 15 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

omnibenchmark/omnibenchmark

The omnibenchmark CLI

Language: Python - Size: 2.15 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 2 - Forks: 3

Cloud-CV/EvalAI

:cloud: :rocket: :bar_chart: :chart_with_upwards_trend: Evaluating state of the art in AI

Language: Python - Size: 63.5 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1,845 - Forks: 862

swcarpentry/make-novice

Automation and Make

Language: Python - Size: 16.8 MB - Last synced at: 1 day ago - Pushed at: 7 days ago - Stars: 158 - Forks: 82

the-nix-way/nome

My Nix home

Language: Nix - Size: 428 KB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 245 - Forks: 20

ropensci/gittargets

Data version control for reproducible analysis pipelines in R with {targets}.

Language: R - Size: 1.5 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 88 - Forks: 1

iterative/example-get-started

Get started DVC project (NLP, random forest)

Language: Python - Size: 22.5 KB - Last synced at: 5 days ago - Pushed at: 12 months ago - Stars: 180 - Forks: 184

tweag/jupyenv

Declarative and reproducible Jupyter environments - powered by Nix

Language: Nix - Size: 10.2 MB - Last synced at: 7 days ago - Pushed at: 9 days ago - Stars: 706 - Forks: 143

tbarbette/npf

Network Performance Framework: easy-to-use experiment manager with automated testing, result collection, and graphing

Language: Python - Size: 4.19 MB - Last synced at: 7 days ago - Pushed at: 18 days ago - Stars: 43 - Forks: 16

codecheckers/codecheck

R package assistant for conducting a CODECHECK

Language: R - Size: 447 KB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 3

maimemo/SSP-MMC-Plus

Optimizing Spaced Repetition Schedule by Capturing the Dynamics of Memory

Language: Python - Size: 43.9 KB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 55 - Forks: 5

luciorq/condathis

Run any CLI tool on a Reproducible Isolated Environment ⚙️⚡

Language: R - Size: 777 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 10 - Forks: 1

workflowhub-eu/about

Website about the project WorkflowHub

Language: HTML - Size: 5.76 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 12 - Forks: 18

leipzig/awesome-reproducible-research

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

Language: Python - Size: 1.42 MB - Last synced at: 6 days ago - Pushed at: 17 days ago - Stars: 343 - Forks: 39

nf-core/references

nf-core/references is a bioinformatics pipeline that build references, for multiple use cases

Language: Nextflow - Size: 868 KB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 14 - Forks: 5

alan-turing-institute/repro-catalogue 📦

A tool to catalogue versions of data, code and results to check the reproducibility of your research project

Language: Python - Size: 242 KB - Last synced at: 7 days ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 0

iterative/demo-bank-customer-churn

Demo DVC project training a classification model on tabular data

Language: Jupyter Notebook - Size: 3.24 MB - Last synced at: 5 days ago - Pushed at: about 1 year ago - Stars: 41 - Forks: 48

jvalegre/aqme

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

Language: Python - Size: 82.3 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 108 - Forks: 26

capitalone/rubicon-ml

Capture all information throughout your model's development in a reproducible way and tie results directly to the model code!

Language: Jupyter Notebook - Size: 25.5 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 132 - Forks: 35

datasnack/datahub

Self-hostable, open-source engine for reproducible data harmonization, dataset building & exploration

Language: Python - Size: 13.4 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 7 - Forks: 2

clementchadebec/benchmark_VAE

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

Language: Python - Size: 42.5 MB - Last synced at: 14 days ago - Pushed at: 10 months ago - Stars: 1,905 - Forks: 174

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.

Language: Python - Size: 19.8 MB - Last synced at: 10 days ago - Pushed at: 5 months ago - Stars: 315 - Forks: 35

formlio/forml

ForML - A development framework and MLOps platform for the lifecycle management of data science projects

Language: Python - Size: 6.32 MB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 106 - Forks: 13

Gaglia88/gsm_repro

Reproducibility experiments for Generalized Supervised Meta-blocking

Language: Python - Size: 60.8 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

Varnasr/EquityStack

A structured repository of Python scripts and Jupyter notebooks for development sector data workflows — including public health, gender equity, women's economic empowerment (WEE), education, and MEL (Monitoring, Evaluation, and Learning). Includes plug-and-play templates, sample data, test coverage, and Colab-ready execution.

Language: Jupyter Notebook - Size: 2.89 MB - Last synced at: 7 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0