DOSE

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 4.6.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Imports: AnnotationDbi, enrichit, ggplot2, GOSemSim, reshape2, yulab.utils
• Install: BiocManager::install("DOSE")

When to Use

• Disease Ontology Analysis: Performing Disease Ontology Semantic and Enrichment analysis as described by the package authors.

When NOT to Use

• For formatting R markdown documents, use knitr because DOSE is strictly for Disease Ontology analysis.

Data Requirements

• Requires loading the package into the R session via library(DOSE).

Key Parameters

• pkg: Used in the Biocpkg function example to format package links.
• tidy: Used in knitr::opts_chunk$set to control code formatting.

Best Practices

• Load the package using library(DOSE).
• Cite the primary publication (Yu et al. 2015) when using DOSE in published research.

Common Pitfalls

• Missing Citation: Forgetting to cite the package in publications; fix by including the citation to Bioinformatics 2015.

Alternatives

• knitr: For document generation and vignette formatting, as it handles markdown chunk options rather than biological enrichment.

Citations

• G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.

References

• Homepage: https://bioconductor.org/packages/DOSE
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/DOSE/inst/doc/DOSE.html

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