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Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
4 references·16 citing·38 second hop
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility (2012)Next-generation sequencing data interpret…Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Galaxy: a comprehensive appro…Accessible Reproducible Research (2010)Accessible Reproducible Resea…Mobyle: a new full web bioinformatics framework (2009)Mobyle: a new full web bioinf…Creating a bioinformatics nation (2002)Creating a bioinformatics nat…The five pillars of computational reproducibility: bioinformatics and beyond (2023)The five pillars of computati…Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv (2019)Sharing interoperable workflo…PhenoMeNal: processing and analysis of metabolomics data in the cloud (2018)PhenoMeNal: processing and an…Experimenting with reproducibility: a case study of robustness in bioinformatics (2018)Experimenting with reproducib…Ten simple rules for making research software more robust (2017)Ten simple rules for making r…Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities (2017)Scientific workflows for comp…Practical Computational Reproducibility in the Life Sciences (2017)Practical Computational Repro…Nonindependence and sensitivity analyses in ecological and evolutionary meta‐analyses (2017)Nonindependence and sensitivi…Investigating reproducibility and tracking provenance – A genomic workflow case study (2017)Investigating reproducibility…Tools and techniques for computational reproducibility (2016)Tools and techniques for comp…Is Most Published Research Really False? (2016)Is Most Published Research Re…Omics Pipe: a community-based framework for reproducible multi-omics data analysis (2015)Omics Pipe: a community-based…Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud (2015)Genomics Virtual Laboratory: …Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics (2014)Mobyle SNAP Workbench: a web-…Dissemination of scientific software with Galaxy ToolShed (2014)Dissemination of scientific s…BioBlend: automating pipeline analyses within Galaxy and CloudMan (2013)BioBlend: automating pipeline…WaveLab and Reproducible Research (1995)Statistical Analyses and Reproducible Research (2007)myExperiment: a repository and social network for the sharing of bioinformatics workflows (2010)CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing (2011)Most computational hydrology is not reproducible, so is it really science? (2016)Design Patterns: Elements of Reusable Object-Oriented Software (1994)Bioconductor: open software development for computational biology and bioinformatics (2004)Nextflow enables reproducible computational workflows (2017)Kepler: An Extensible System for Design and Execution of Scientific Workflows (2004)Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Galaxy: A platform for interactive large-scale genome analysis (2005)GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians (2021)Snakemake—a scalable bioinformatics workflow engine (2012)Scientific workflows: Past, present and future (2017)FAIR Computational Workflows (2019)Cochrane Handbook for Systematic Reviews of Interventions (2008)The PRISMA Statement for Reporting Systematic Reviews and Meta-Analyses of Studies That Evaluate Health Care Interventions: Explanation and Elaboration (2009)Conducting Meta-Analyses in R with the metafor Package (2010)Gender differences in individual variation in academic grades fail to fit expected patterns for STEM (2018)Research Weaving: Visualizing the Future of Research Synthesis (2018)Quantitative evidence synthesis: a practical guide on meta-analysis, meta-regression, and publication bias tests for environmental sciences (2023)Jupyter Notebooks – a publishing format for reproducible computational workflows (2016)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines (2019)Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing (2019)A Practical Guide to Metabolomics Software Development (2021)Design of Experiments (1936)The Logic of Scientific Discovery. (1959)Design and Analysis of Computer Experiments (1989)Reproducible and replicable pain research: a critical review (2018)Recommendations to enhance rigor and reproducibility in biomedical research (2020)EntropyHub: An open-source toolkit for entropic time series analysis (2021)1,500 scientists lift the lid on reproducibility (2016)Streamlining data-intensive biology with workflow systems (2021)Empowering bioinformatics communities with Nextflow and nf-core (2025)BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case (2005)Counting Species: Biopower and the Global Biodiversity Census (2008)Bioboxes: standardised containers for interchangeable bioinformatics software (2015)
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References

  • 2010Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences3,455 cited
  • 2002Creating a bioinformatics nation343 cited
  • 2009Mobyle: a new full web bioinformatics framework310 cited
  • 2010Accessible Reproducible Research308 cited

Cited by

  • 2017Nonindependence and sensitivity analyses in ecological and evolutionary meta‐analyses267 cited
  • 2014Dissemination of scientific software with Galaxy ToolShed257 cited
  • 2017Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities181 cited
  • 2016Tools and techniques for computational reproducibility169 cited
  • 2017Practical Computational Reproducibility in the Life Sciences158 cited
  • 2018PhenoMeNal: processing and analysis of metabolomics data in the cloud150 cited
  • 2015Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud118 cited
  • 2017Ten simple rules for making research software more robust111 cited
  • 2013BioBlend: automating pipeline analyses within Galaxy and CloudMan96 cited
  • 2019Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv81 cited

Only edges whose both ends are imported exist here. Widen the year window, or show the whole map. Back to the work

  • 2023The five pillars of computational reproducibility: bioinformatics and beyond80 cited
  • 2018Experimenting with reproducibility: a case study of robustness in bioinformatics77 cited
  • 2017Investigating reproducibility and tracking provenance – A genomic workflow case study76 cited
  • 2016Is Most Published Research Really False?76 cited
  • 2015Omics Pipe: a community-based framework for reproducible multi-omics data analysis75 cited
  • 2014Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics72 cited