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Essential guidelines for computational method benchmarking
16 references·1 citing·36 second hop
Essential guidelines for computational method benchmarking (2019)Essential guidelines for computational me…Systematic benchmarking of omics computational tools (2019)Systematic benchmarking of om…Improving the usability and archival stability of bioinformatics software (2019)Improving the usability and a…Challenges and recommendations to improve the installability and archival stability of omics computational tools (2019)Challenges and recommendation…The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018)The Galaxy platform for acces…Putting benchmarks in their rightful place: The heart of computational biology (2018)Putting benchmarks in their r…Meta-research: Why research on research matters (2018)Meta-research: Why research o…Bioconda: sustainable and comprehensive software distribution for the life sciences (2018)Bioconda: sustainable and com…iCOBRA: open, reproducible, standardized and live method benchmarking (2016)iCOBRA: open, reproducible, s…Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research (2015)Ten Simple Rules for Reducing…Reproducible research in statistics: A review and guidelines for the Biometrical Journal (2015)Reproducible research in stat…Ten Simple Rules for Reproducible Computational Research (2013)Ten Simple Rules for Reproduc…A Plea for Neutral Comparison Studies in Computational Sciences (2013)A Plea for Neutral Comparison…Snakemake—a scalable bioinformatics workflow engine (2012)Snakemake—a scalable bioinfor…Reproducible Research in Computational Science (2011)Reproducible Research in Comp…Why Most Published Research Findings Are False (2005)Why Most Published Research F…Why Most Published Research Findings Are False (2005)Why Most Published Research F…Reproducible and replicable comparisons using SummarizedBenchmark (2018)Reproducible and replicable c…Taverna: a tool for the composition and enactment of bioinformatics workflows (2004)Galaxy: A platform for interactive large-scale genome analysis (2005)Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences (2010)Good enough practices in scientific computing. (2017)Preferred reporting items for systematic reviews and meta‐analyses in ecology and evolutionary biology: a PRISMA extension (2021)Improving the quality of reports of meta-analyses of randomised controlled trials: the QUOROM statement (1999)Meta-analysis of Observational Studies in Epidemiology A Proposal for Reporting (2000)The CONSORT statement: revised recommendations for improving the quality of reports of parallel-group randomised trials (2001)False-Positive Psychology (2011)Power failure: why small sample size undermines the reliability of neuroscience (2013)Estimating the reproducibility of psychological science (2015)1,500 scientists lift the lid on reproducibility (2016)A manifesto for reproducible science (2017)The nf-core framework for community-curated bioinformatics pipelines (2020)The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update (2024)How Many Scientists Fabricate and Falsify Research? A Systematic Review and Meta-Analysis of Survey Data (2009)The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta‐analyses (2016)Research Weaving: Visualizing the Future of Research Synthesis (2018)Examining overlap of included studies in meta‐reviews: Guidance for using the corrected covered area index (2019)How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship (2019)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update (2016)Singularity: Scientific containers for mobility of compute (2017)Sustainable data analysis with Snakemake (2021)A review of bioinformatic pipeline frameworks (2016)Over-optimism in benchmark studies and the multiplicity of design and analysis options when interpreting their results (2021)Genomic reproducibility in the bioinformatics era (2024)Packaging and containerization of computational methods (2024)A Replication Crisis in Methodological Research? (2020)Overinterpretation of findings in machine learning prediction model studies in oncology: a systematic review (2023)Increasing value and reducing waste in research design, conduct, and analysis (2014)Reproducibility in Science (2014)An introduction to Docker for reproducible research (2015)Nextflow enables reproducible computational workflows (2017)Sustainable data analysis with Snakemake (2021)The New Statistics (2013)The ethics of algorithms: Mapping the debate (2016)
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References

  • 2005Why Most Published Research Findings Are False10,471 cited
  • 2005Why Most Published Research Findings Are False4,702 cited
  • 2018The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update3,659 cited
  • 2012Snakemake—a scalable bioinformatics workflow engine2,775 cited
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  • 2013A Plea for Neutral Comparison Studies in Computational Sciences143 cited
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  • 2015Reproducible research in statistics: A review and guidelines for the Biometrical Journal

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35 cited
  • 2018Putting benchmarks in their rightful place: The heart of computational biology31 cited
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    • 2018Reproducible and replicable comparisons using SummarizedBenchmark8 cited