Question

RNA-Seq Workflow Example (not "airway") for R

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detroit.drive • 0

@detroitdrive-16757

Last seen 5.5 years ago

Hi Everyone,

It seems like every example (on the web) for an RNA-Seq workflow uses the "airway" dataset. Does anyone know of a Bioconductor RNA-Seq workflow example that's something other than airway?

Very respectfully, DD

RNA-Seq Workflow • 1.2k views

ADD COMMENT • link updated 5.5 years ago by Gordon Smyth 51k • written 5.5 years ago by detroit.drive • 0

score 2 · Accepted Answer · 2019-05-28

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Gordon Smyth 51k

@gordon-smyth

Last seen just now

WEHI, Melbourne, Australia

edgeR User's Guide (click on the edgeRUsersGuide.pdf link. Gives complete code for 5 RNA-seq case studies.)
limma User's Guide (click on the usersguide.pdf link. Gives 2 RNA-seq case studies, using same datasets as for the edgeR User's Guide.)
RnaSeqGeneEdgeRQL workflow package (click on the "html" link)
https://f1000research.com/articles/5-1438
RNAseq123 workflow package (click on the "html" link)
https://f1000research.com/articles/5-1408
http://bioinf.wehi.edu.au/RNAseqCaseStudy

ADD COMMENT • link 5.5 years ago Gordon Smyth 51k

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Many thanks Gordon. The bottom three links are just what I was seeking.

V/r, DD

ADD REPLY • link 5.5 years ago detroit.drive • 0

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It appears that the 'fission' package is very similar to 'airway'. Is it possible to follow the workflow steps posted on the web for airway but replace the data with fission?

ADD REPLY • link 5.5 years ago detroit.drive • 0