Bioconductor

[fruce-ki]

Look into submitting RATs to Bioconductor.

• R CMD CHECK flags
• R CMD BiocCheck
• DESCRIPTION : update author fields.
• DESCRIPTION : add biocViews field with at least 2 values (https://bioconductor.org/packages/release/BiocViews.html).
• Consider if it is appropriate to accommodate SummarizedExperiment as an input option (https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html).
• NAMESPACE : Review the @imports across all source code, replace with @importFrom wherever possible.
• NEWS : Create this file, to track changes (consult ?news) for format. Cannot be plaintext.
• Revise vignettes : Bioconductor styling
• Revise vignettes : Minimise/remove non executable chunks
• Revise vignettes : add Introduction section.
• Revise vignettes : add Installation
• Revise vignettes : add sessionInfo()
• Revise vignettes : re-style third-party package citations to match their citation().
• Switch to BiocParallel
• Break down multi-page chunks of code.

[fruce-ki]

https://github.com/Bioconductor/Contributions

[fruce-ki]

Notes to self:

• GenomicFeatures instead of rtracklayer to import GTF/GFF and convert to tx2gene index.
• tximport for tx abundance import and gene-level summarisation.