reproducible-science

There are 7 repositories under reproducible-science topic.

• IDSIA / sacred

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

  infrastructuremachine-learningmongodbpythonreproducibilityreproducible-researchreproducible-science
  Language:Python 4287
• nextflow

  nextflow-io / nextflow

  A DSL for data-driven computational pipelines

  awsbioinformaticsclouddataflowdockergroovyhellohpcnextflowpipelinepipeline-frameworkreproducible-researchreproducible-sciencesgesingularitysingularity-containersslurmworkflow-engine
  Language:Groovy 2878

• 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.

  cloud-nativecontainercontainershpclinuxparallelportabilityportablereproduciblereproducible-sciencerootless-containerssciencesingularitysingularity-container
  Language:Go 2557

• openwdl / wdl

  Specification for the Workflow Description Language (WDL).

  bioinformaticscloudopenwdlreproducibilityreproducible-sciencewdlworkflow
  807

• benmarwick / rrtools

  rrtools: Tools for Writing Reproducible Research in R

  quartoquarto-templaterreproducibilityreproducible-paperreproducible-researchreproducible-scienceresearch-compendiumresearch-paperresearch-projectresearch-tool
  Language:R 686

• showyourwork / showyourwork

  A workflow for reproducible and open scientific articles

  continuous-integrationlatexopen-sourcereproducible-researchreproducible-sciencescientific-papersscientific-workflows
  Language:TeX 589

• mit-ll-responsible-ai / hydra-zen

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

  configurableconfigurationdataclassesdeep-learningdynamic-configurationmachine-learningmachinelearningpytorchpytorch-lightningreproducibilityreproducible-sciencescalableyaml-configuration
  Language:Python 367
• awesome-reproducible-research

  leipzig / awesome-reproducible-research

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

  awesomeawesome-listreproducibilityreproducible-analysisreproducible-researchreproducible-sciencereproducible-workflows
  Language:Python 341
• 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.

  archivingcomputational-sciencedockerhacktoberfestlinuxnyuptracepythonreproducibilityreproducible-researchreproducible-sciencereprounzipreprozipsciencescientific-computingvagrant
  Language:Python 312
• containerit

  o2r-project / containerit

  Package an R workspace and all dependencies as a Docker container

  dockerdockerfilerreproducible-researchreproducible-science
  Language:R 291

• genecell / single-cell-papers-with-code

  Papers with code for single cell related papers

  single-cellscrna-seqscrna-seq-analysisreproducible-researchreproducible-sciencesingle-cell-omicssingle-cell-atac-seqpaper-with-codesingle-cell-rna-seq
  281

• Kaixhin / FGLab

  Future Gadget Laboratory

  machine-learningreproducible-researchreproducible-science
  Language:HTML 223

• InsightSoftwareConsortium / ITK-Wasm

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

  asmjsemscriptenimaginginput-outputinsight-toolkititkitk-modulejavascriptopen-sciencereproducible-sciencevtkwasiwasmwebassembly
  Language:Python 208
• shournal

  tycho-kirchner / shournal

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

  bashcommand-trackercomputational-sciencefile-trackerlowlevelprovenancereproducibilityreproducible-researchreproducible-scienceshellzsh
  Language:C++ 194

• nanxstats / liftr

  🐳 Containerize R Markdown documents for continuous reproducibility

  containerizationdockerdynamic-documentsknitrliftrreproducible-researchreproducible-sciencermarkdownstatistical-computing
  Language:R 172

• alan-turing-institute / TCPDBench

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

  benchmarkbenchmark-suitechange-detectionchange-pointchange-point-detectionchangepointreproducible-paperreproducible-researchreproducible-science
  138
• Sarek

  SciLifeLab / Sarek

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

  nextflowworkflowpipelinebioinformaticsgenomicscancernext-generation-sequencingdockersingularityreproducible-sciencereproducible-researchcontainersgermlinegermline-variantssomaticsomatic-variants
  Language:Nextflow 133

• mgalardini / pyseer

  SEER, reimplemented in python 🐍🔮

  bacteriagwask-merreimplementationreproducible-science
  Language:Python 120

• everware / everware

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

  reproducible-researchreproducible-sciencejupyter-notebookdocker
  Language:Python 116

• deanmarchiori / analysis-flow

  Data Analysis Workflows & Reproducibility Learning Resources

  data-analysisreproducibilityreproducible-data-sciencereproducible-sciencetoolingworkflow
  113

• commontk / dcmjs

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

  dicomjavascriptimagingopen-sciencereproducible-sciencewebassemblyasmjswasmemscriptendcmtk
  Language:CMake 109

• 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.

  job-submissionpipelineprovenancepythonreproducibilityreproducible-scienceversioningvisualizationvtkworkflow
  Language:Python 103

• I2PC / scipion

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

  electron-microscopycryo-emsingle-particle-analisysstructural-biologyworkflowreproducible-scienceusabilityimage-processingpythonc-plus-plus
  Language:Python 80

• faroit / reproducible-audio-research

  List of Reproducible Audio Research Papers

  curated-listreproducible-researchreproducible-scienceaudio
  74

• Kaixhin / FGMachine

  Future Gadget Machine

  machine-learningreproducible-researchreproducible-science
  Language:JavaScript 69

• geoscixyz / em

  Electromagnetic methods in geophysics - open educational resources.

  geophysicseducationelectromagneticsopen-sciencereproducible-sciencegeoscience
  Language:HTML 67

• nuest / ten-simple-rules-dockerfiles

  Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

  dockerfilesten-simple-rulesreproducible-researchreproducible-sciencereproducible-paperopen-sciencecontainerizationcontainerisation
  Language:TeX 65

• fmalmeida / MpGAP

  Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

  hybrid-assembliesilluminapipelinegenome-assemblypolishpacbionanoporeunicyclerspadesflyecanureproducible-researchreproducible-sciencepilonnextflowworkflow
  Language:Nextflow 58

• cernanalysispreservation / analysispreservation.cern.ch

  Source code for the CERN Analysis Preservation portal

  big-datadigital-librarydigital-repositoryflaskhacktoberfestinvenioinveniosoftwarejson-schemapythonreproducible-researchreproducible-scienceresearch-dataresearch-data-life-cycle-managementresearch-data-managementresearch-data-repositoryreusable-artifacts
  Language:Python 44

• ecoinfAEET / Reproducibilidad

  Reproducible Science: what, why, how

  reproducible-sciencerrmarkdowndata-scienceversion-controlreproducibility
  Language:RMarkdown 43

• rostools / prodigenr

  Project directory generator R package

  rstatsreproducible-researchreproducible-scienceopen-sourceopen-sciencereproducibilityproject-managementrstudiousethisdevtoolscran
  Language:R 43

• empiricalci / emp

  :microscope: Empirical CLI

  scienceaidockerartificial-intelligencereproducible-researchreproducible-sciencebenchmark-frameworkbenchmarking
  Language:JavaScript 42

• calekochenour / remote-sensing-textbook

  Textbook that provides JavaScript and Python code to create open reproducible remote sensing analyses and workflows in Google Earth Engine.

  google-earth-enginejavascriptjupyter-notebookspythonremote-sensingreproducible-sciencereproducible-workflowsscientific-computingtextbook
  Language:HTML 41

• opengeophysics / testipynb

  unit-testing for a collection of jupyter notebooks using nbconvert

  jupyterreproducible-researchreproducible-sciencetesting
  Language:Python 41

• brainhack-school2020 / abide-fmri

  Repository for the Brainhack School 2020 team working with fMRI and ABIDE data to train machine learning models.

  abide-dataautismbrainhack-schoolcross-validationcv-classifierfmrigroup-kfold-cross-validationjupyter-notebookskfold-cross-validationleave-one-out-cross-validationnilearnplotlypreparation-scriptproject-managementreproducible-scienceresting-state-fmriscikitlearn-machine-learningsupport-vector-classification
  Language:Jupyter Notebook 40

• tilburgsciencehub / website

  Learn to work more efficiently on empirical research projects.

  data-analysisdata-scienceeconomicsmarketing-automationquantitative-economicsreproducible-scienceresearchresearch-paper
  Language:HTML 40