GitHub topics: reproducible-science

Repositories

RePlasma/RePlasma.github.io

Reproduced papers in Plasma Physics and beyond

Language: HTML - Size: 1.36 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 0

shawntz/fmri

a (work in progress) attempt to transform the stanford memory lab's internal fmri preprocessing scripts into a generalizable template for consistency within and across lab projects

Language: Shell - Size: 314 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 0

ReproducibiliTea-org/reproducibiliTea

Website for the ReproducibiliTea Journal Club and Podcast

Language: HTML - Size: 6.81 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 8 - Forks: 26

nextflow-io/nextflow

A DSL for data-driven computational pipelines

Language: Groovy - Size: 58.2 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 2,922 - Forks: 684

InsightSoftwareConsortium/ITK-Wasm

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

Language: Python - Size: 230 MB - Last synced at: 4 days ago - Pushed at: 11 days ago - Stars: 212 - Forks: 53

calkit/calkit

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

Language: Python - Size: 8.67 MB - Last synced at: 4 days ago - Pushed at: 4 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: 4 days ago - Pushed at: 6 months ago - Stars: 4,297 - Forks: 382

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.

Language: Go - Size: 34.8 MB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 2,566 - Forks: 427

opengisci/opengisci.github.io

Open Geographic Information Science Curriculum

Language: HTML - Size: 15 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

tilburgsciencehub/website

Learn to work more efficiently on empirical research projects.

Language: HTML - Size: 233 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 40 - Forks: 48

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: 5 days ago - Pushed at: 16 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: 11 days ago - Pushed at: 11 days ago - Stars: 14 - Forks: 5

showyourwork/showyourwork

A workflow for reproducible and open scientific articles

Language: TeX - Size: 13.7 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 600 - Forks: 49

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: 8 days ago - Pushed at: 5 months ago - Stars: 315 - Forks: 35

carpentries-incubator/ReproducibleResearch

7 Steps towards Reproducible Research

Language: HTML - Size: 11.9 MB - Last synced at: 3 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 4

shawntz/eyeris

A flexible, extensible, and reproducible pupillometry preprocessing framework in R

Language: R - Size: 79.5 MB - Last synced at: 15 days ago - Pushed at: 17 days ago - Stars: 4 - Forks: 3

arunisaac/ravanan

High-reproducibility CWL runner powered by Guix

Language: Scheme - Size: 1.1 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 10 - Forks: 0

temuller/piscola

Supernova light-curve fitting code

Language: Python - Size: 134 MB - Last synced at: 18 days ago - Pushed at: 3 months ago - Stars: 8 - Forks: 7

TC22-Team/TC22

TC22 website

Language: HTML - Size: 2.84 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 2 - Forks: 0

fmalmeida/ngs-preprocess

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

Language: Nextflow - Size: 5.27 MB - Last synced at: 6 days ago - Pushed at: 11 months ago - Stars: 34 - Forks: 5

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.

Language: Python - Size: 141 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 20 - Forks: 6

tucca-cellag/tucca-rna-seq

[UNDER-CONSTRUCTION] TUCCA's RNA-Seq Snakemake Workflow for Cellular Agriculture Projects

Language: Python - Size: 845 KB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 1 - Forks: 0

UCSB-Library-Research-Data-Services/project-data-management

Good enough practices to manage and preserve your project data

Language: HTML - Size: 5.87 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 2 - Forks: 0

mit-ll-responsible-ai/hydra-zen

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

Language: Python - Size: 23.1 MB - Last synced at: 28 days ago - Pushed at: about 1 month ago - Stars: 372 - Forks: 17

geoscixyz/em

Electromagnetic methods in geophysics - open educational resources.

Language: HTML - Size: 422 MB - Last synced at: about 22 hours ago - Pushed at: 3 months ago - Stars: 69 - Forks: 66

benmarwick/rrtools

rrtools: Tools for Writing Reproducible Research in R

Language: R - Size: 4.87 MB - Last synced at: 27 days ago - Pushed at: 7 months ago - Stars: 685 - Forks: 86

francois-rozet/dawgz

Unleash the true power of scheduling

Language: Python - Size: 84 KB - Last synced at: 7 days ago - Pushed at: about 1 month ago - Stars: 29 - Forks: 4

alan-turing-institute/TCPDBench

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

Size: 154 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 139 - Forks: 28

VolodiaPG/giraff

Using functions and auctions for a sustainable Fog model

Language: Rust - Size: 222 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 1

nuest/sensebox-binder

A reproducible analysis of environmental data - from hardware to plot

Language: Jupyter Notebook - Size: 1.97 MB - Last synced at: about 1 month ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

SORTEE-Github-Hackathon/manuscript

This repository implements an automated system to write our collaborative manuscript, while tracking changes and contributions.

Language: HTML - Size: 55.3 MB - Last synced at: 28 days ago - Pushed at: about 2 years ago - Stars: 23 - Forks: 17

BioDataScience-Course/sdd-umons-2024

Science des données biologiques I, UMONS (2024-2025)

Language: R - Size: 15.3 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

BioDataScience-Course/sdd-umons2-2024

Science des données biologiques II, UMONS (2024-2025)

Language: R - Size: 2.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

pythonhealthdatascience/rap_template_r_des

Template reproducible analytical pipeline (RAP) for simple R discrete-event simulation (DES) model.

Language: R - Size: 68.4 MB - Last synced at: 29 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1

o2r-project/containerit

Package an R workspace and all dependencies as a Docker container

Language: R - Size: 1.62 MB - Last synced at: 8 days ago - Pushed at: about 3 years ago - Stars: 289 - Forks: 29

Pakillo/ReproducibleScience

Short course on reproducible science: what, why, how

Language: RMarkdown - Size: 43.2 MB - Last synced at: 2 days ago - Pushed at: 4 months ago - Stars: 22 - Forks: 0

openplantpathology/Reproducibility_in_Plant_Pathology

A systematic/quantitative review of articles, which provides a basis for identifying what has been done so far in the field of plant pathology research reproducibility and suggestions for ways to improving it.

Language: TeX - Size: 2.06 GB - Last synced at: 6 days ago - Pushed at: 9 months ago - Stars: 23 - Forks: 6

everhartlab/sclerotinia-366

Analysis for "Population structure and phenotypic variation of *Sclerotinia sclerotiorum* from dry bean (*Phaseolus vulgaris*) in the United States"

Language: Shell - Size: 165 MB - Last synced at: 5 days ago - Pushed at: about 7 years ago - Stars: 9 - Forks: 6

nanxstats/liftr

🐳 Containerize R Markdown documents for continuous reproducibility

Language: R - Size: 4.96 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 171 - Forks: 20

VisTrails/VisTrails

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.

Language: Python - Size: 134 MB - Last synced at: 26 days ago - Pushed at: over 7 years ago - Stars: 104 - Forks: 45

hsf-training/hsf-training-reana-webpage

Let's make your analysis reproducible with REANA

Language: Makefile - Size: 4.84 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 3

supernnova/SuperNNova

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

Language: Python - Size: 6.38 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 31 - Forks: 8

cernanalysispreservation/analysispreservation.cern.ch

Source code for the CERN Analysis Preservation portal

Language: Python - Size: 37.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 44 - Forks: 31

petebachant/repro-qiu-et-al-2024

Reproducing the results of Qiu et al. (2024) "Decarbonized energy system planning with high-resolution..."

Language: Python - Size: 2.94 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

faroit/reproducible-audio-research

List of Reproducible Audio Research Papers

Size: 6.54 MB - Last synced at: about 1 month ago - Pushed at: about 7 years ago - Stars: 74 - Forks: 11

nuest/ten-simple-rules-dockerfiles

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Language: TeX - Size: 19.6 MB - Last synced at: 5 days ago - Pushed at: over 4 years ago - Stars: 65 - Forks: 15

tillbiskup/labinform

Python components of the laboratory information system LabInform

Language: Python - Size: 138 KB - Last synced at: 19 days ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

openwdl/brand

Branding materials for the Workflow Description Language and OpenWDL.

Size: 6.33 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 1

RecSysEvaluation/IntentAwareRS

This is the official repository of the paper "A Worrying Reproducibility Study of Intent-Aware Recommendation Models"

Language: Python - Size: 122 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

ropensci/lightr

Import spectral data and related metadata in R

Language: R - Size: 6.63 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 13 - Forks: 1

tdayris/fair_rnaseq_salmon_quant

Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon

Language: Python - Size: 183 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

sjackman/open-science

:microscope: Open, reproducible science using Make, RMarkdown and Pandoc

Language: CSS - Size: 1.99 MB - Last synced at: about 1 month ago - Pushed at: over 10 years ago - Stars: 9 - Forks: 16

cthoyt/pystow

👜 Easily pick a place to store data for your Python code.

Language: Python - Size: 295 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 35 - Forks: 6

martibosch/cookiecutter-data-snake

Reproducible data science template using Python, snakemake, mamba and more :snake:

Language: Python - Size: 244 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 2 - Forks: 1

andreas-zeller/papers-as-modules

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

Language: Jupyter Notebook - Size: 573 KB - Last synced at: 5 days ago - Pushed at: almost 7 years ago - Stars: 20 - Forks: 2

pythonhealthdatascience/stars-reproduce-hernandez-2015

Assessing the computational reproducibility of Hernandez et al. 2015 as part of STARS.

Language: TeX - Size: 15.4 MB - Last synced at: 29 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

nrybowski/ns3-sim

Artefacts for the paper "Evaluating OSPF Convergence with ns-3 DCE"

Language: C++ - Size: 180 KB - Last synced at: about 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

quant-aq/aeromancy

⚗️ Aeromancy: A framework for performing reproducible AI and ML

Language: Python - Size: 1.27 MB - Last synced at: about 4 hours ago - Pushed at: 7 months ago - Stars: 11 - Forks: 1

fgcz/fcc

An automated rule-based processing tool for life science data.

Language: Python - Size: 104 KB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

psychtek/ContainR

The goal of ContainR is to enable easier container development for computational reproducibility by RStudio Rocker-Versioned stacks to create a Docker image of a project.

Language: R - Size: 2.38 MB - Last synced at: 4 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

VIDA-NYU/reproducibility-news

Currated reproducibility news displayed on reproduciblescience.org

Language: Python - Size: 2.43 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 13 - Forks: 7

aeturrell/example-reproducible-research

This has been prepared as an example of reproducible research for the online book Coding For Economists.

Language: Python - Size: 98.6 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 3

datasnakes/awesome-reproducible-R

An awesome list of resources for reproducible research in R. Includes a table of comparison for different tools.

Language: R - Size: 16.6 KB - Last synced at: 10 days ago - Pushed at: 5 months ago - Stars: 13 - Forks: 0

rostools/prodigenr

Project directory generator R package

Language: R - Size: 3.26 MB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 43 - Forks: 13

tillbiskup/aspecd

Python framework for handling spectroscopic data focussing on reproducibility

Language: Python - Size: 4.64 MB - Last synced at: 30 days ago - Pushed at: 5 months ago - Stars: 9 - Forks: 0

EDS-Bioinformatics-Laboratory/ENCORE

ENCORE: Enhancing Computational Reproducibility

Language: Python - Size: 20.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 0

pythonhealthdatascience/rap_des

Documentation supporting template reproducible analytical pipelines (RAP) for simple python and R discrete-event simulation (DES) models.

Size: 60.6 MB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

alan-turing-institute/CSV_Wrangling

Repository for reproducibility of the CSV file project

Language: TeX - Size: 6.2 MB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 28 - Forks: 6

tillbiskup/cwepr

A Python package based on the ASpecD framework for handling cwEPR data.

Language: Python - Size: 20 MB - Last synced at: 29 days ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1

tillbiskup/fitpy

A Python package for fitting models to (spectroscopic) data.

Language: Python - Size: 367 KB - Last synced at: about 1 hour ago - Pushed at: 5 months ago - Stars: 2 - Forks: 1

tillbiskup/trepr

A Python package based on the ASpecD framework for handling TREPR data.

Language: Python - Size: 19.9 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

BioDataScience-Course/sdd-umons3-2024

Science des données biologiques III & IV, UMONS (2024-2025)

Language: R - Size: 3.44 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

deanmarchiori/analysis-flow

Data Analysis Workflows & Reproducibility Learning Resources

Size: 37.1 KB - Last synced at: 5 months ago - Pushed at: about 4 years ago - Stars: 113 - Forks: 9

openwdl/wdl

Workflow Description Language - Specification and Implementations

Size: 5.81 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 776 - Forks: 307

scienxlab/unmap

Unmap data from a pseudocolor image, with or without knowing the colormap.

Language: Python - Size: 15.2 MB - Last synced at: 5 days ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 2

o2r-project/architecture

Architecture and overarching documentation for o2r microservices

Language: Makefile - Size: 7.81 MB - Last synced at: about 2 months ago - Pushed at: almost 4 years ago - Stars: 11 - Forks: 4

emsejournal/openscience

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

Size: 112 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 33 - Forks: 11

pythonhealthdatascience/stars-eom-rcc Fork of nice-digital/NICE-model-repo

Modifications to the "Exeter Oncology Model: Renal Cell Carcinoma edition (EOM-RCC)" as part of STARS work package 3.

Language: R - Size: 49.5 MB - Last synced at: 3 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 0

idso-fa1-pathology/k8s-cluster-env

Environment Configuration for Kubernetes Cluster Usage

Language: Dockerfile - Size: 34.2 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 1

basiralab/RG-Select

Quantifying the Reproducibility of Graph Neural Networks using Multigraph Brain Data

Language: Python - Size: 2.37 MB - Last synced at: 10 days ago - Pushed at: almost 3 years ago - Stars: 8 - Forks: 2

SciLifeLab/Sarek Fork of nf-core/sarek 📦

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

Language: Nextflow - Size: 43.8 MB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 133 - Forks: 7

Related Keywords

reproducible-science 256 reproducible-research 138 reproducibility 80 python 33 open-science 32 r 28 data-science 22 bioinformatics 22 reproducible-paper 21 docker 18 pipeline 13 rstats 12 workflow 12 rmarkdown 12 jupyter-notebook 11 science 11 machine-learning 11 data-analysis 11 reproducible-experiments 10 rstudio 10 reproducible 9 research 8 snakemake 7 teaching-materials 7 reproducible-analysis 6 github 6 singularity 6 conda 6 git 6 latex 6 research-compendium 6 scientific-computing 6 template 6 genomics 6 deep-learning 6 binder 5 geophysics 5 version-control 5 hacktoberfest 5 computational-physics 5 ecology 5 nextflow 5 spectroscopy 5 hpc 5 conda-environment 5 research-paper 4 open-source 4 computational-science 4 automation 4 plasma-physics 4 markdown 4 rna-seq 4 simulation 4 workshop 4 quarto 4 discrete-event-simulation 4 kubernetes 3 snakemake-workflows 3 data-processing 3 electron-paramagnetic-resonance 3 reproducible-workflows 3 microbiology 3 bioinformatics-pipeline 3 statistics 3 project-management 3 nyucds 3 research-tool 3 dataset 3 ngs 3 scrna-seq 3 replicability 3 healthcare 3 good-practices 3 chemistry 3 dockerfile 3 pytorch 3 remote-sensing 3 cloud 3 workflows 3 tidyverse 3 javascript 3 slurm 3 visualization 3 python3 3 docker-image 3 tutorial 2 evolution 2 workflow-engine 2 open-data 2 ecological-modelling 2 pipeline-framework 2 healthcare-analysis 2 reproducible-analytical-pipeline 2 reproducible-analytical-pipelines 2 simmer 2 simulation-framework 2 simulation-model 2 simulation-modeling 2 genome-assembly 2 phd 2

GitHub topics: reproducible-science

pythonhealthdatascience/stars-eom-rcc Fork of nice-digital/NICE-model-repo

SciLifeLab/Sarek Fork of nf-core/sarek 📦

benmarwick/researchcompendium 📦