reproducible-science

There are 6 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 4156
• nextflow

  nextflow-io / nextflow

  A DSL for data-driven computational pipelines

  bioinformaticsworkflow-enginepipelinepipeline-frameworknextflowcloudgroovysgeslurmawsdockersingularityhpcsingularity-containersreproducible-sciencereproducible-researchdataflowhello
  Language:Groovy 2539

• 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.

  containerscontainersingularity-containerportablelinuxhpcparallelsingularitysciencereproduciblereproducible-scienceportabilityrootless-containerscloud-native
  Language:Go 2498

• openwdl / wdl

  Workflow Description Language - Specification and Implementations

  bioinformaticscloudcromwellopenwdlreproducibilityreproducible-sciencewdlworkflow
  723

• benmarwick / rrtools

  rrtools: Tools for Writing Reproducible Research in R

  rreproducible-researchreproducibilityreproducible-scienceresearch-projectresearch-paperresearch-toolreproducible-paperresearch-compendiumquartoquarto-template
  Language:R 661

• showyourwork / showyourwork

  A workflow for reproducible and open scientific articles

  continuous-integrationlatexopen-sourcereproducible-researchreproducible-sciencescientific-papersscientific-workflows
  Language:TeX 533
• 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.

  reprozipcomputational-sciencereprounzippythonreproducibilitylinuxsciencescientific-computingarchivingreproducible-researchreproducible-scienceptracedockervagrantnyuhacktoberfest
  Language:Python 295
• awesome-reproducible-research

  leipzig / awesome-reproducible-research

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

  awesome-listawesomereproducibilityreproducible-researchreproducible-sciencereproducible-analysisreproducible-workflows
  Language:Python 294
• containerit

  o2r-project / containerit

  Package an R workspace and all dependencies as a Docker container

  dockerdockerfilerreproducible-researchreproducible-science
  Language:R 285

• mit-ll-responsible-ai / hydra-zen

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

  configurationmachine-learningdataclassesdynamic-configurationyaml-configurationpytorchpytorch-lightningreproducibilityreproducible-sciencescalableconfigurablemachinelearningdeep-learning
  Language:Python 274

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

  Papers with code for single cell related papers

  paper-with-codereproducible-researchreproducible-sciencescrna-seqscrna-seq-analysissingle-cellsingle-cell-atac-seqsingle-cell-omics
  254

• Kaixhin / FGLab

  Future Gadget Laboratory

  machine-learningreproducible-researchreproducible-science
  Language:HTML 222

• InsightSoftwareConsortium / itk-wasm

  High performance spatial analysis in a web browser, Node.js, and across programming languages and hardware architectures

  input-outputinsight-toolkitemscriptenreproducible-scienceopen-sciencejavascriptimagingitkwebassemblyasmjswasmitk-modulevtkwasi
  Language:Python 177

• nanxstats / liftr

  🐳 Containerize R Markdown documents for continuous reproducibility

  dockerreproducible-researchrmarkdowncontainerizationdynamic-documentsreproducible-scienceknitrliftrstatistical-computing
  Language:R 169
• shournal

  tycho-kirchner / shournal

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

  shellbashcommand-trackerzshlowlevelfile-trackerreproducible-researchcomputational-scienceprovenancereproducibilityreproducible-science
  Language:C++ 159
• 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 132

• 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
  123

• everware / everware

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

  dockerjupyter-notebookreproducible-researchreproducible-science
  Language:Python 116

• deanmarchiori / analysis-flow

  Data Analysis Workflows & Reproducibility Learning Resources

  data-analysisreproducibilityreproducible-data-sciencereproducible-sciencetoolingworkflow
  110

• commontk / dcmjs

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

  asmjsdcmtkdicomemscriptenimagingjavascriptopen-sciencereproducible-sciencewasmwebassembly
  Language:CMake 108

• 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.

  reproducibilitypythonvisualizationvtkversioningworkflowprovenancereproducible-sciencepipelinejob-submission
  Language:Python 101

• mgalardini / pyseer

  SEER, reimplemented in python 🐍🔮

  gwasbacteriak-merreimplementationreproducible-science
  Language:Python 96

• 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 75

• Kaixhin / FGMachine

  Future Gadget Machine

  machine-learningreproducible-researchreproducible-science
  Language:JavaScript 69

• faroit / reproducible-audio-research

  List of Reproducible Audio Research Papers

  curated-listreproducible-researchreproducible-scienceaudio
  68

• geoscixyz / em

  Electromagnetic methods in geophysics - open educational resources.

  geophysicseducationelectromagneticsopen-sciencereproducible-sciencegeoscience
  Language:HTML 62

• nuest / ten-simple-rules-dockerfiles

  Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

  containerisationcontainerizationdockerfilesopen-sciencereproducible-paperreproducible-researchreproducible-scienceten-simple-rules
  Language:TeX 60

• fmalmeida / MpGAP

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

  hybrid-assembliesilluminapipelinegenome-assemblypolishpacbionanoporeunicyclerspadesflyecanureproducible-researchreproducible-sciencepilonnextflowworkflow
  Language:Nextflow 51

• 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 43

• rostools / prodigenr

  Project directory generator R package

  crandevtoolsopen-scienceopen-sourceproject-managementreproducibilityreproducible-researchreproducible-sciencerstatsrstudiousethis
  Language:R 43

• empiricalci / emp

  :microscope: Empirical CLI

  aiartificial-intelligencebenchmark-frameworkbenchmarkingdockerreproducible-researchreproducible-sciencescience
  Language:JavaScript 42

• ecoinfAEET / Reproducibilidad

  Reproducible Science: what, why, how

  data-sciencerreproducibilityreproducible-sciencermarkdownversion-control
  Language:RMarkdown 41

• opengeophysics / testipynb

  unit-testing for a collection of jupyter notebooks using nbconvert

  jupyterreproducible-researchreproducible-sciencetesting
  Language:Python 41

• alapo / Literate-Programming

  This is the repository for the Literate Programming Workshop

  rreproducible-sciencerstudioworkshop
  Language:R 39

• hakyimlab / ukbrest

  ukbREST: efficient and streamlined data access for reproducible research of large biobanks

  biobankuk-biobankreproducible-researchreproducible-sciencereproducibility
  Language:Python 37

• 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 36