Question

Examples of concise description of NGS and bioinformatics (with DESEq2 or edgeR) in M&M of biological paper

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Vladimir Krasikov ▴ 90

@vladimir-krasikov-5097

Last seen 5.1 years ago

Dear Experts,

I wonder if somebody contributed to or met biological! paper, where NGS and following bioinformatics are just one of the many methods used, and thus bioinformatics part is described in few concise paragraphs readable by biologists, but understandable by bioinformaticians. Preferably related to DESEq2 or edgeR NGS data analysis pipelines

Regards

Vladimir

deseq2 edgeR • 929 views

ADD COMMENT • link updated 7.2 years ago by Gordon Smyth 51k • written 7.2 years ago by Vladimir Krasikov ▴ 90

score 3 · Answer 1 · 2017-09-06

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Gordon Smyth 51k

@gordon-smyth

Last seen 52 minutes ago

WEHI, Melbourne, Australia

There are lots of examples -- we and other groups do this all the time. Here's a few recent examples from our group that happen to be open access:

https://doi.org/10.1371/journal.pbio.2000731

https://doi.org/10.1016/j.celrep.2016.08.056

https://doi.org/10.1038/ncomms13353

ADD COMMENT • link 7.2 years ago Gordon Smyth 51k

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Thank you, Gordon. I should come to idea to have a look myself for the papers where you or Michael Love are coauthors.

ADD REPLY • link 7.2 years ago Vladimir Krasikov ▴ 90

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After a full day of searching I am still not able to find any good experimental papers which utilise the DESeq2 workflow in couple of concise paragraphs.

ADD REPLY • link 7.2 years ago Vladimir Krasikov ▴ 90