Creating reproducible pharmacogenomic analysis pipelines
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Summary
Pharmacogenomic workflows in the Common Workflow Language are developed to process two breast cancer datasets in a reproducible and transparent manner and combine both pharmacological and molecular profiles into a portable data object that can be used for future analyses in cancer research.
- Type
- preprint
- Published
- 2019-04-19
- Cited by
- 7
- References
- 47
- Access
- Open access
- OpenAlex
- https://openalex.org/W2938899814
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:145878975
Keywords
Workflow, Computer science, Scalability, Pipeline (software), Identifier
References
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- Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome
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- Statistical Analysis of Big Data on Pharmacogenomics
- Modeling precision treatment of breast cancer
- Overall C as a measure of discrimination in survival analysis: model specific population value and confidence interval estimation
- Research Objects: Towards Exchange and Reuse of Digital Knowledge
- Bioconductor: open software development for computational biology and bioinformatics
- Subtype and pathway specific responses to anticancer compounds in breast cancer
- MVN: An R Package for Assessing Multivariate Normality
- Leveraging Big Data to Transform Target Selection and Drug Discovery
- Revisiting inconsistency in large pharmacogenomic studies
- Functional genomic Landscape of Human Breast Cancer drivers, vulnerabilities, and resistance
- PharmacoGx: an R package for analysis of large pharmacogenomic datasets
- Volume and Value of Big Healthcare Data
- Exploring Big Data Analysis: Fundamental Scientific Problems
- The FAIR Guiding Principles for scientific data management and stewardship
- Next Generation Sequencing Technology and Genomewide Data Analysis: Perspectives for Retinal Research
Cited by
- ORCESTRA: a platform for orchestrating and sharing high-throughput pharmacogenomic analyses
- Lightweight Distributed Provenance Model for Complex Real–world Environments
- Data platforms for open life sciences–A systematic analysis of management instruments
- Interactive NLU-Powered Ontology-Based Workflow Synthesis for FAIR Support of HPC
- Toward a common standard for data and specimen provenance in life sciences
- Computational modeling of drug response identifies mutant-specific constraints for dosing panRAF and MEK inhibitors in melanoma
- Computational Modeling of Drug Response Identifies Mutant-Specific Constraints for Dosing panRAF and MEK Inhibitors in Melanoma
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