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davismcc / scaterPaperExtras

Discussion board for modifications to the scater paper
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Page 2: Implementation: Paragraph 1 #6

Closed LTLA closed 8 years ago

LTLA commented 8 years ago

The package builds on many other R packages: ...

There is far too much stuff listed here. Just do:

The package builds on many other R packages, including Biobase and BiocGenerics for core Bioconductor functionality (Huber et al. 2015); destiny (Angerer et al., 2015) and Rtsne (Krijthe, 2015) for dimensionality reduction; and edgeR (Robinson et al., 2010) and limma (Ritchie et al., 2015) for model fitting and statistical analyses. A full set of dependencies is provided in the Supplementary Materials.

This should cut down your references by a lot, probably.

kieranrcampbell commented 8 years ago

While I agree with Davis that it's good to cite packages used I agree that there are too many listed here. Might be worth citing Hadley Wickham once though since half the packages are his (e.g. plotting with ggplot2 [cite]).

davismcc commented 8 years ago

Yep, very sensible changes. I've switched this to Aaron's text plus a short sentence mentioning ggplot2 with a citation.